The Obama administration turned to its top officials to tout democracy and political transparency for Egypt, a message that took on a hollow tone as the Egyptian military installed a new leader for the country and began rounding up its ousted president and his supporters.

Secretary of State John Kerry, Defence Secretary Chuck Hagel and national security adviser Susan Rice were among those who briefed President Barack Obama on Thursday on their calls to counterparts in Egypt, Israel, Turkey and other U.S. partners in the region.

The calls conveyed “the importance of a quick and responsible return of full authority to a democratically elected civilian government as soon as possible,” said Bernadette Meehan, a spokeswoman for the White House National Security Council.

The U.S. officials also pushed for what Ms. Meehan called “a transparent political process that is inclusive of all parties and groups” and urged that those in charge of Egypt’s government avoid any arbitrary arrests of Egyptian President Mohamed Morsy and his supporters. Avoiding violence by any group or party was also part of their message, she said in an emailed statement.

Behind the scenes, the U.S. was signalling to Egypt and its allies that it accepts the military’s decision to depose Mr. Morsy, and was hoping that what fills the vacuum of power would be more favourable to U.S. interests and values than Mr. Morsy’s Islamist government. But those hopes were tempered by very real concerns that a newly emboldened military would deal violently with the Muslim Brotherhood, sending Egyptian society further into chaos and making reconciliation more difficult.

In spite of U.S. urging, Egyptian authorities arrested and detained the leader of the Muslim Brotherhood, General Guide Mohammed Badie, on Thursday. Mr. Morsy, a leading member of the Brotherhood, and at least a dozen presidential aides already had been placed under house arrest.

The military also oversaw the swearing-in of Adly Mansour, the head of the Supreme Constitutional Court, as Egypt’s interim president. The Muslim Brotherhood declared it wouldn’t work with the new government and called for a wave of protests.

Mr. Morsy’s ouster also threatened a divided reaction in Congress. One view tended to support the Egyptian military’s action because of the long-time partnership between the U.S. and Egyptian military officials as well as perceived threats by Mr. Morsy to the type of democracy Egyptians aspired to during their 2011 revolution. Another view, however, noted that U.S. law called for an end to aid to a country if a military deposed its democratically elected government, even amid promises of a return of power to its people.

Mr. Obama on Wednesday, while notably not calling Mr. Morsy’s ouster a coup, said he was ordering the government to assess what the developments portended for aid to Cairo.

The U.S. considers the $1.5 billion a year it sends Egypt to be a critical U.S. national security priority.

The administration faced difficult choices amid the ongoing crisis. If it denounced the ouster of Morsi, it could be accused of propping up a ruler who had lost public support. Yet, if it supported the military’s action, the administration could be accused of fomenting dissent or could lose credibility on its commitment to the democratic process.

The administration is acting as if it accepts what happened in Egypt and actually believes it could turn out for the best with Mr. Morsy no longer in charge. At the same time, officials are attempting to keep their distance, laying down markers for what they want to see in the long term while leaving it up to the military to make sure that happens.

But the White House may also be concerned that in the short term, the situation could spiral out of control, with the military using the clamouring in the streets as an excuse to confront the Muslim Brotherhood with excessive force. In bringing up U.S. aid in conversations with Egyptians without cutting it off, the U.S. leaves itself room to escalate the situation if need be, but also to work with Egypt’s new government if it moves in the right direction.

After Mr. Morsy’s ouster on Wednesday, Mr. Obama said the U.S. would “not support particular individuals or political parties,” acknowledging the “legitimate grievances of the Egyptian people” while also observing that Mr. Morsy won his office in a legitimate election.

“We believe that ultimately the future of Egypt can only be determined by the Egyptian people,” Obama said. “Nevertheless, we are deeply concerned by the decision of the Egyptian armed forces to remove President Morsy and suspend the Egyptian constitution.”

Egyptian military leaders have assured the Obama administration that they were not interested in long-term rule following their toppling of Mr. Morsy. The chairman of the U.S. military’s Joint Chiefs of Staff, Gen. Martin Dempsey, told CNN after Mr. Morsy’s ouster that the U.S. had been assured by the Egyptian military that U.S. citizens there would be protected. Still, the State Department ordered all nonessential U.S. diplomats and the families of all American Embassy personnel to leave Egypt.

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