A spokesman for a pro-Brotherhood alliance put the death toll amongst its followers at about 1,400.

The turmoil has alarmed the United States and the European Union, but Israel and some Gulf Arab states led by Saudi Arabia have pressed the West not to punish Cairo’s new rulers.

Qatar, the only Gulf state seen as sympathetic to Mursi, sent another tanker of liquefied natural gas to energy-strapped Egypt this week despite the army takeover.

Badie was charged in July with incitement to murder in connection with protests before Mursi’s ouster and is due to stand trial on August 25 along with his two deputies.

Footage shown on local media showed the bearded leader sitting grim-faced in a grey robe near a man with a rifle following his detention in Cairo in the early hours.

The release of the images seemed designed to humiliate the Brotherhood chief, whose arrest means the group’s top echelon is now behind bars, with other leaders dropping out of sight.

The Brotherhood’s newspaper reported that the movement had named Mahmoud Ezzat, an influential former deputy to Badie, as its temporary leader.

However, a spokesman for the Brotherhood’s political party, Khaled Hanafi, said he could neither confirm or deny the report. Ezzat has not appeared in public since Mursi was removed.

After decades as an outlawed movement, the Brotherhood emerged as the best-drilled political force following President Hosni Mubarak’s fall in pro-democracy protests in 2011.

Now the state accuses it of al-Qaeda-style militancy and subversion, charges it vehemently denies.

Founded in 1928, the Islamist group used its organisational muscle to secure victory for Mursi last year’s presidential election. It says it has about a million members among Egypt’s 85 million people, as well as offshoots across the Arab world.

The whereabouts of many other senior Brotherhood politicians are unknown. Those who had been posting frequently on social media have stopped in the last two days. Arrests have extended beyond Cairo, netting provincial leaders of the movement.

The Brotherhood condemned the detention of Badie, whose 38-year-old son was killed in Cairo clashes on Friday.

“When the hand of oppression extends to arrest this important symbol, that means the military coup has used up everything in its pocket and is readying to depart,” it said.

The state news agency said Badie was now in Cairo’s Tora prison, where other Brotherhood leaders are held. Mubarak is also jailed there, though legal moves to release him are afoot.

A court will examine a bail petition for Mubarak, 85, on Wednesday, judicial sources said.

Freedom for the man who ruled Egypt for 30 years could stir more political tension in the most populous Arab nation, where his former Islamist foes are now being hunted down.

Mursi has been held in an undisclosed location since the army toppled him following mass protests against him.

Tamarod, the youth organisation which orchestrated the street campaign against Mursi, hailed Badie’s detention as “an important step on the path of the revolution, fighting terrorism and dismantling the terrorist group by arresting its leaders”.

The Brotherhood, which renounced violence decades ago, has promised peaceful resistance to the army takeover.

United Nations Secretary-General Ban Ki-moon called on the authorities to release Mursi, or at least ensure a transparent process for him. He also said on Monday that the “very limited” political space for the Muslim Brotherhood should be expanded.

The United States urged Egypt not to ban the Brotherhood, an option floated in the past week by the interim prime minister.

Jeffrey Feltman, UN under-secretary for political affairs, arrived in Egypt on Tuesday for talks that Ban had said would focus on initiatives to restore peace and forge reconciliation.

Egypt began three days of official mourning for 25 policemen killed on Monday by suspected Islamist militants in the Sinai near the desert border with Israel. State television carried emotional demands for retribution against the Brotherhood.

The off-duty policemen were returning to their barracks in Rafah when militants attacked them. The government said the men had been forced from their vehicles and shot in cold blood.

The army said on Tuesday it had captured 11 “terrorist elements” in Sinai, including two Palestinians.

The United States, a close ally of Egypt since it signed a peace treaty with Israel in 1979, said on Monday it was still reviewing whether to freeze any of its US$1.55 billion annual aid package to Egypt, which mostly funds US weapons supplies.

Washington also voiced concern about the deaths on Sunday of 37 detainees who authorities said were suffocated by tear gas during an escape attempt. The circumstances remain unclear.

The pro-Brotherhood alliance condemned the Sinai attack, which it accused the “security apparatus of the coup government” of carrying out to divert attention from the deaths of the 37 men who had been in transit to Abu Zabal prison near Cairo.

The alliance also called for a consumer boycott of businesses and states that “support the bloody military coup”.

Foreign ministers of the European Union, another donor to Egypt, meet in Brussels on Wednesday to discuss how it might apply its influence for a peaceful compromise.

However, Egypt’s interim government, buoyed by considerable popular support, as well as diplomatic backing from Israel and Saudi Arabia, which has promised to make up for any shortfall in Western aid, has said it will resist any outside pressure.