In the jungles of Borneo, the proboscis monkeys are long-nosed, pot-bellied and sad-faced. They look like ageing clowns (until you notice the erections: apparently proboscis harems are considerable affairs). Of an evening, they sit in the meranti trees, legs splayed, hands on knees, chewing with an air of resignation through the never-ending leaf salad that surrounds them. The males sport a white ruff that makes them look as if they're in pyjamas - a ginger onesie perhaps.

The proboscis offers a humbling reminder of the basic instincts we share, the selfish gene and the biological imperative, stripped of all artifice. Perhaps they are too easy to anthropomorphise as they frown, chew their lips and scratch their behinds. But if we recognise kinship, or feel any sense of responsibility, we should be concerned about the fate of our cute, lovable, randy cousins. Because they may not be around much longer. The proboscis is one of nine species of monkeys and apes whose extinction may well occur in our lifetime, on our watch.

Which is why I am aboard a swanky boat in the Indonesian archipelago. My fellow passengers are supporters of the Durrell Wildlife Conservation Trust. Founded by the late British naturalist and writer Gerald Durrell, the trust is committed to protecting endangered species.

Saving such animals is normally quite hard work. All over the world, dedicated field workers are living in shacks of plywood and tar paper, struggling daily through steamy jungles, battling leeches and loggers, hoping to protect shrinking habitats and prevent lawless poaching, which are the chief threats to many species' survival. Our part in the crusade is rather less arduous: we sunbathe, we snorkel, we eat too much, we make a serious dent in the nautical wine cellar. Occasionally we listen to a few agreeable lectures, but our cruise ship does the legwork, ferrying us in style from tropical islands to jungle rivers to visit three of the creatures the trust is hoping to sustain - the Bornean orangutan, the Komodo dragon and the Bali starling. Part of our fares for this sybaritic expedition is going towards sustaining the trust.

The ship was a few days into its schedule when I joined at Kumai, a dusty river town on the southern shore in Kalimantan. I waited on a rickety dock while mosquitoes feasted on my ankles until, sometime before midnight, a cluster of distant lights appeared in the darkness. As they drew nearer, they formed themselves into a small cruise ship, the Orion.

EARLY THE NEXT MORNING, we have an appointment with the orangutans. Leaving the Orion at anchor, we head up the Sekonyer river in klotoks, traditional double-decker wooden boats. Smoke from slash-and-burn agriculture hangs over the river like early mist. The clearance of the great forests for palm-oil plantations is the continuing scandal of Kalimantan, with half the orangutan habitat lost over the past 20 years as a result.

We are travelling into the depths of the Tanjung Puting National Park, more than 4,000 sq km of dry tropical forest, wetlands and mangrove swamps. There may be fewer than 50,000 orangutans left in Kalimantan and most live within the boundaries of this park, which is home to the Camp Leakey orangutan sanctuary.

Dragonflies the size of small birds hover above the mud-coloured current. Mangrove herons fly upstream. A troupe of macaque monkeys pauses mid-acrobatics to watch us drift by. We spot flycatchers making mud nests the size of egg cups while the guide eagerly points out the poisonous fruit that the Dayaks, the indigenous tribespeople of Borneo, use to murder one another.

From the landing stage at Camp Leakey, we follow paths through the dappled light of the forest. Insects drone. Birdsong tumbles out of the dense foliage. From a tree adorned with several of Borneo's 3,000 species of orchids, a moon-faced gibbon looks down on us. Gibbons are heart-throbs. Forming pair bonds for life, the males sing to the females every morning. Orangutans, like the proboscis, are less romantic.

Orangutans are Asia's only great apes. Their intelligence is the stuff of legend and now, increasingly, of science. In a zoo in Atlanta, in the United States, orangutans are playing touch-screen computer games. In California, a female orangutan has learnt sign language. But, like many intelligent creatures, they come with emotional baggage. Unlike chimps and gorillas, they are solitary and do not appear to enjoy groups. The only genuine bonding is between a mother and her child, who keeps hold of the apron strings until it is about four or five years old. Fathers take no part in caring for the young. Studies have shown that secondary males, the ones the alphas boss, suffer unusually high levels of stress.

After a mile or so, we arrive at the feeding station, and settle down to wait. The whole arrangement has the curious air of a film premiere - a rope, a phalanx of long-lensed cameras, a handful of guides to keep us in line, an air of hushed expectation as we wait for the stars. The raised feeding platform takes the place of the red carpet. For the celebrities in Tanjung Puting, the lure is not fame but two enormous baskets of very ripe-looking bananas.

There are whispers of anticipation: the orangutans are coming, they aren't coming, one has been spotted in a tree half a mile away … We crane our necks, we stand on tiptoes, we lean over the ropes. Then, suddenly, the first orangutan - a mother with a youngster clinging to her tummy - materialises on the edge of the clearing, her features familiar from a dozen wildlife films.

The first ape is soon joined by several others. They tuck into the bananas with an air of entitlement. They ignore the assembled fans. Their ears are cocked to a much more important world - the jungle behind them. And then it seems they have heard something. Quite suddenly they rise from their haunches, vacate the platform and melt away into the forest.

"Tom," whispers one of the guides. "Big Tom is coming."

Big Tom is the star turn. He swings down out of a tree in an elegant slow-motion arc, then crosses the feeding platform with a John Wayne swagger as camera shutters click furiously. His enormous cheek flanges and his long coat - the kind of shaggy orange afghan that alpha males wore to 1970s pop festivals - announces his status. Weighing as much as 18 stone and not a long way short of six foot, Tom gazes at the black bananas, unimpressed.

We already know so much about Tom, particularly the gossip about his out-of-control libido. A sign along the path issued a stark warning: "Never stand between the alpha male and a female." No fear of that as his arrival has cleared the forest.

Tom generally announces his presence with the "long call", a Tarzan-like cry that echoes through the jungle. It tells receptive females he is on the pull and warns lesser males to make themselves scarce. But Tom cannot be everywhere. Secondary males copulate with Tom's females when his back is turned. Perhaps it is this that contributes to their high stress levels. Anyone would be a bundle of nerves if they were cuckolding Tom.

On the walk back to the river, I encounter a female orangutan perched in a tree by the path. Her toddler is breastfeeding. She has had her bananas. It is a moment of reflection.

We stand looking at one another, as close as if we were across a dinner table. Orangutans are one of our nearest relations; along with chimps and gorillas we are members of the same elite taxonomic family - the Hominidae. In Malay, " orangutan" means simply "man of the forest". They say we can trace our ancestry back some 14 million years to a shared source, some hairy man-ape creeping through the green gloom of a forest.

With an orangutan, the similarities of movement and expression are startling. But it is her eyes that are most striking. We gaze at one another almost like old friends. She tilts her head, her eyes searching mine. What we both see is an expression of thoughtful curiosity, the eyes of a being that has a life beyond mere biological imperative.

We sail home on a darkening river where swallows skim the surface and kingfishers flash across the bow. A hornbill clatters into a tree above crocodiles pretending to snooze on a sandbank while fireflies wink among the greenery like lost stars.

The next morning we set course across the Java Sea to the long scattering of islands that stretch eastward to Papua New Guinea. Our evenings are a floating house party: excellent dinners, fine wine and good companions. Our days become a round of delightful shore excursions. We lounge on deserted beaches and study antediluvian turtles. One morning we make our way to the floating markets of Banjarmasin, a waterworld where everything comes and goes by boat - vegetables, schoolchildren, firewood, the post. Another day, on West Nusa Tenggara, we go to the buffalo races, a deranged cross between a Happy Valley meet and mud wrestling.

In Sumbawa Besar we visit the royal palace of Dalam Loka, a glorious teak barn of a building raised on 99 stilts and built without a single piece of ironmongery. Here, royalty is in decline. The current sultan, Muhammad Kaharuddin IV, who once worked as a bank clerk in Jakarta, grew up in a modest 1930s bungalow with a rusty flagpole out front.

On our days at sea there are lectures - Lee Durrell, Gerald's widow and a first-rate naturalist, gives a couple of excellent talks - but no one could really compete with Harry Christensen, a proper ocker Aussie who has been sailing these waters for years. Permanently barefoot, with a dress code steering towards Aussie formal - shorts and T-shirt - his oratorical manner is that of an evangelical preacher wrestling with the devil.

At full throttle, flinging superlatives around with reckless abandon, Christensen tells us about the Komodo dragon - how its venom induces shock and heart failure in its victims, how it dislocates its jaws like a snake to devour large prey, how it is a miniature replica of a much larger Jurassic ancestor. "AMAZING!" he raves, flapping his arms like a man trying to escape his own body. "These dragons inspired the legends of King Kong!"

It is a credit to the Komodo dragon that it manages to live up to Christensen's billing. On Komodo island, a small group of us set off through open woodlands accompanied by a guard who looks about 12. He is armed with a forked stick, which doesn't seem sufficient should it be necessary to slay a dragon.

Deer ghost through the shadows among dry-leaf litter. Firebirds chatter and tiny flying lizards glide between the tamarind trees. A purple drongo bird with a fan tail poses glamorously on a branch overlooking a bay of hump-backed islands. We pause to examine some dragon poo on the trail; quite fresh, according to our boy guide. A herd of black pigs suddenly and noisily breaks cover, and the woman next to me almost jumps into my arms.

After half an hour or so, we come upon a lone male dragon loitering in a grove of trees. Measuring close to 10 feet, his hide consists of heavy armoured scales. He turns his head to get a better look at us, standing nervously some 20 feet away. Let's just say this is not the thoughtful gaze of my new best friend, the orangutan. The dragon's tongue, a forked affair a couple of feet long, flicks in and out. I can see the venom dripping from its mouth. It is flecked with blood. Perhaps it has just eaten one of its children. Infanticide is one of the habits that reinforce the Komodo's fearsome reputation.

Our final port of call is the tiny island of Nusa Penida, just east of Bali. For some time, the Durrell Wildlife Conservation Trust has been supporting a project here to save the Rothschild's mynah, otherwise known as the Bali starling. The beauty of the species - pure white with a glorious crest and a marvellous song - is leading to its dramatic decline; it is captured in large numbers for the caged-bird trade popular in Southeast Asia. At one point, at the turn of the millennium, there were thought to be only six of the birds left in the wild.

The whole boat has been invited to a ceremony conducted in the Hindu temple, to mark the release of four of the birds into the wild. The thinking is that a religious blessing might make the pet trade think twice about recapturing them.

We disembark on a sand beach on a palm-fringed shore. Local dignitaries have gathered, including the rotund regent of Nusa Penida, a ceremonial colonel adorned with enough braid to hang several deserters, and the local MP, who has opted for wraparound shades, giving him the air of a minor Mafia hitman.

Perched on the shore, with waves washing its wall, the temple consists of a series of shrines surrounded by fantastical stone carvings, yellow umbrellas and roofs of thatched horse hair. In an outer court, a burly fellow is blessing witches with a bucket of holy water. In the inner sanctum, a white-robed priest tinkles a small bell to let the gods know we are ready, and the prayers begin.

They go on for a bit. Afterwards, the dignitaries stand in a row with the decorated starling boxes and release the newly blessed birds. They flutter up into a blue sky, circle the temple, then fly away into their new world. Sadly for them, they are obliged to share it with us.

We must speak up for the proboscis monkey, the orangutan, the Komodo dragon and the Bali starling; the degradation of the environment, the collapse of habitats and the threat to more than 16,000 species of endangered wildlife is a threat to us all.

The Telegraph UK