“In the last five years, radiation levels have been reduced substantially, and we can say that the plant is stable now,” said Akira Ono, the Tepco plant superintendent.

Efforts to contain the contamination have progressed, according to Tepco, including the completion on Tuesday of a subterranean ice wall around the plant that will freeze the ground and stop leakage. Moves to decommission the plant – a process that could take 30 or 40 years, Ono estimated – are getting underway.

People will be allowed to return to their homes in the nearby town of Naraha next month, and to Tomioka, even closer to the plant, next year. For now, Tomioka and neighbouring Okuma are ghost towns, lined with shops, fast-food restaurants and gambling parlours that haven’t had a customer in five years. Bicycles lean near front doors and flower pots sit empty on window sills.

A sign on the road to the plant showed a radiation reading of 3.37 microsieverts per hour, at the upper end of safe. At a viewing spot overlooking the reactor buildings, it shot past 200. Both readings are hundreds of times lower than they were a couple of years ago.

But one huge question remains: what is to be done with all the radioactive material?

There’s the groundwater that is flowing into the reactor buildings, where it becomes contaminated. It has been treated – Tepco says it can remove 62 nuclides from the water, including strontium, which can burrow into bones and irradiate tissue. It cannot filter out tritium, a radioactive isotope of hydrogen that can be used to make nuclear bombs but is not considered especially harmful to humans.

The water initially was stored in huge bolted tanks in the aftermath of the disaster, but the tanks have leaked highly contaminated radioactive water into the sea on an alarming number of occasions.

Now Tepco is building more secure welded tanks to hold the water, theoretically for up to 20 years. There are now about 1,000 tanks holding 750,000 tonnes of contaminated water, with space for 100,000 tonnes more. The company says it hopes to increase capacity to 950,000 tonnes within a year or two, as well as halve the amount of water that needs to be stored from the current 300 tonnes per day.

The company hoped to have the new ice wall working next month, but on Wednesday, Japan’s nuclear watchdog blocked the plan, saying the risk of leakage was still too high.

The options for getting rid of the contaminated water include trying to remove the tritium from it before letting it run into the sea; evaporating it, as was done at Three Mile Island, the Pennsylvania plant that melted down in 1979; and injecting it deep into the ground, using technology similar to that used to extract shale gas. A government task force is considering which option to choose.

“These all have different advantages and disadvantages; they have different costs and different social acceptance,” said Seiichi Suzuki, manager of tank construction at the plant.

Then there’s the radioactive soil that has been collected from areas around the Fukushima Daiichi plant during clean-up efforts. More than 700 million cubic feet of soil – enough to fill 8,000 Olympic-sized swimming pools – has been packed into large black plastic bags and is being stored, row upon row, in local fields.

More than 700 of the bags, which contain radioactive caesium isotopes, were swept away during floods last year, some ending up in rivers 161km away. The government has said that 99.8 per cent of the soil can be recycled.

Finally, and most problematically, there’s the nuclear fuel from the plant itself.

The fuel that melted down remains in containment vessels in its reactors, and this part of the plant is so dangerous to humans that robots are used to work there. Getting to this fuel and removing it safely is a task that will take decades.

Asked about the decommissioning process, Ono said the work was about 10 per cent done.

“The biggest challenge is going to be the removal of the nuclear fuel debris,” he said. “We don’t even know what state the debris is in at the moment.”

Japan does not have a nuclear waste dump, and there is vehement resistance to disposing of contaminated material on land.

As a result, one of the options the government is considering is building a nuclear waste dump under the seabed, about eight miles off the Fukushima coast. It would be connected to the land by a tunnel so it would not contravene international regulations on disposing of nuclear waste into the sea. A government study group is set to report on that proposal by the end of the summer.

Many groups, from fishermen to anti-nuclear activists, staunchly oppose the idea of burying the radioactive material at sea in such a seismically active area.

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“At some point it would leak and affect the environment,” said Hideyuki Ban, co-director of the Citizens’ Nuclear Information Centre. “Some say it’ll be fine, as it will be diluted in the ocean, but it’s unclear whether it will be diluted well. If it gets into fish, it could end up on someone’s table.”

Aileen Mioko Smith, executive director of Green Action, a Kyoto-based anti-nuclear group, agreed.

“The seabed is just like land. It’s not flat, but has mountains and valleys,” she said. “Japan sits on multiple tectonic plates and is earthquake-prone. It’s too easy to think, ‘If not on land, how about the seabed?’”