It has been one week, and nobody knows where the former president of Egypt is. Mohamed Morsi is being detained, along with at least seven of his top aides, held incommunicado. The authorities promise, “He is in a safe place.” But safe where? They refuse to say. He has not been charged with any crime.

Authorities have issued arrest warrants for hundreds of other Muslim Brotherhood members and supporters, including the group’s spiritual leader, known as the “supreme guide.” He and nine other senior Islamist officials were accused Wednesday of provoking the violence that led Egyptian security forces to fatally shoot more than 50 pro-Morsi demonstrators Monday.

The warrants come as authorities continue to round up the top leaders of the Muslim Brotherhood and its political arm, the Freedom and Justice Party, which saw its hold on the presidency and several top ministries end after 368 days when Morsi’s government was ousted last week in a military coup backed by millions of Egyptians who had taken to the streets.

The mass arrests and the continued detention of Morsi and his aides are exactly the type of behavior that the Obama administration has warned Egypt’s military leadership against. But the crackdown shows how little influence Washington has been able to exert here since the generals proved they remain the nation’s preeminent force.

Morsi himself was accused of selectively using the judicial system to prosecute opponents, as was his predecessor, Hosni Mubarak, who was ousted in early 2011. Now human rights advocates say that Egypt’s new rulers may be doing the same.

“The biggest casualty of the last couple of years has been the idea of a neutral judiciary in Egypt, and in the last few days, that tradition continues,” said Heba Morayef, an Egypt researcher for the group Human Rights Watch.

Morayef said that in the Mubarak years, Muslim Brotherhood leaders were arrested for “membership in an illegal organization.” Now they are being arrested for allegedly inciting violence. “It is very clever,” she said, adding that there may be evidence to prove such charges in some cases but not in others.

A close relative of a top Morsi aide who disappeared on the night of the coup said the families of missing Brotherhood leaders have been unable to contact their loved ones since.

“My brother was allowed a couple of phone calls over the past week, just to say, ‘I am safe,’ and ‘I’m okay,’ ” said the relative, who spoke on the condition of anonymity out of fear for the safety of those in detention. But when the relative pressed for more details, the answer was always, “I cannot say.”

“We don’t have any information on where they are,” the relative said. “We don’t have any information on who’s detaining them. We don’t have an accurate account of the numbers.”

The relative also said that the families of the detained have received phone calls from men who they think are working for Egypt’s security services. “They have been threatening the families not to seek any international support,” the relative said.

Ahmed Aly, a spokesman for the country’s armed forces, said Tuesday that Morsi and his aides had been moved from the Republican Guard headquarters in Cairo, where their supporters believed them to be, to an undisclosed location.

Gehad el-Haddad, a Muslim Brotherhood spokesman, tweeted that the arrest warrants issued Wednesday were a “politically motivated” attempt to dismantle the continued protests scattered across Cairo. Pro-Morsi demonstrators say they will maintain their vigil until he is reinstated.

Officials deny crackdown

Egyptian officials denied that a crackdown on the Muslim Brotherhood is underway. “There are no exceptional measures being taken against any political force,” said Badr Abdelatty, a spokesman for the Ministry of Foreign Affairs. “Those who are using violence will be dealt with within the existing judicial system. Nothing more, nothing less.”

Egypt’s justice system allows for imprisonment without trial for up to six months under a provision that lets prosecutors slap any suspect with repeated 15-day detentions.

An official at the Interior Ministry said that although arrest warrants were issued Wednesday for the Brotherhood’s supreme guide, Mohammed Badie, and his deputy, Mahmoud Ezzat, they were not yet in custody.

“This has to be done carefully,” said the official, who spoke on the condition of anonymity because he was not authorized to talk to foreign reporters. He suggested that police were not ready to wrest Badie and Ezzat from the arms of their supporters.

Badie and the others were sought for “inciting violence” in connection with the Monday protest outside the Republican Guard headquarters that turned deadly, he said.

In a discussion with foreign reporters Wednesday, spokesmen for Egypt’s military, Foreign Ministry and state information service argued that Morsi’s ouster was not a coup and that Monday’s violence was not the military’s fault.

The officials showed reporters a video, set to dramatic music, that included a montage of aerial footage of anti-Morsi demonstrators on the day that millions demonstrated to call for his exit. Aly, the military’s spokesman, narrated over footage from Monday’s violence, which appeared to show pro-Morsi demonstrators opening fire on troops with birdshot and dropping pieces of broken toilet bowls off a rooftop.

Government spokesmen, however, did not provide video footage from the first two hours of the tumult — between 4 and 6 a.m. — when Brotherhood witnesses say security forces attacked them with live gunfire.

“We were not ready at 4 o’clock. We did not have our cameras ready,” Aly said.

When pressed about the location and condition of Morsi, government officials grew agitated. “He is not charged with anything up till now. But you know, the security situation — you have to put in mind public order,” Abdelatty said. “This is a country! The public order is at stake right now! People are inciting their followers to go to be martyred, to break into military establishments. So what are you asking for?”

The spokesmen showed video clips of pro-Morsi demonstrators threatening Egypt’s armed forces with violence and civil war. Brotherhood leaders have called for “an uprising” against the military, although they have also urged supporters to remain peaceful.

Transition plan criticized

The clash between the military and the Brotherhood has come as the country’s new civilian authorities have sought to project an air of normalcy. Interim President Adly Mansour on Tuesday appointed a new prime minister and vice president, and he outlined a path to quick elections, an amended constitution and a return to democracy.

That plan, however, continued to meet with criticism Wednesday — not only from the Brotherhood, but also from groups that had supported Morsi’s ouster. The National Salvation Front, an umbrella group representing Morsi’s political opponents, said Wednesday that it did not agree with all elements of the transition plan and that it had not been consulted. It stopped short of outright rejection.

Sharaf al-Hourani contributed to this report.