GWEN IFILL: Egypt's military government dealt another blow to the Muslim Brotherhood today, taking the group's supreme leader into custody.
Margaret Warner begins our coverage.
MARGARET WARNER: Authorities charged the group's general guide, Mohammed Badie, with inciting violence in the aftermath of former President Mohammed Morsi's ouster early last month.
Muslim Brotherhood officials condemned the move.
KHALED HANAFI, anti-coup alliance member (through interpreter): With regards to the arrest of our leader, we move as an alliance. He runs peaceful protests. He's a symbol. And we are greatly saddened about him being taken to prison without being prosecuted, without any legal procedures. This will affect us all.
MARGARET WARNER: But, on the street, some found it welcome news.
WOMAN (through interpreter): It is a great achievement. I was so happy. He is a nasty individual, an enemy, horrid.
MARGARET WARNER: Badie is just one of many Muslim Brotherhood officials who have been detained since the government moved against two large pro-Morsi encampments last Wednesday.
Nearly 1,000 people are estimated to have died in the violence that day and in confrontations since then. The Muslim Brotherhood places the death toll near 1,400. The turmoil has prompted Egypt's international partners, including the United States and the European Union, to reexamine their aid to Cairo.
The United States, which gives Egypt $1.3 billion a year in military assistance, has delayed delivery of four F-16 fighter jets and pulled out of the Bright Star joint military exercises in Egypt set for September.
But Gulf allies Saudi Arabia, Kuwait, and the United Arab Emirates have stepped in with some $12 billion in monetary and fuel aid to Egypt since Morsi was deposed July 3. Monday, the Saudi foreign minister promised to fill any financial gaps left by other countries suspending aid.
On Sunday, Egyptian Foreign Minister Nabil Fahmy said Egypt welcomed the help from other quarters, saying, "We are not looking to replace one friend with another, but we will look out to the world and continue to establish relations with other countries so we have options."
On the NewsHour last night, Egypt's ambassador to the U.S., Mohamed Tawfik, said America's aid program is important for both nations.
MOHAMED TAWFIK, Egyptian Ambassador to the United States: We would like it to continue to be a win/win situation, particularly since we agree on the objective. We have the same objective. We want to see a democratic system in place in Egypt.
MARGARET WARNER: There's some confusion about the current state of the program. The Daily Beast first reported today that, according to Vermont Senator Patrick Leahy's office, the Obama administration has suspended the assistance temporarily.
White House spokesman Josh Earnest insisted that wasn't true.
JOSH EARNEST, White House Deputy Press Secretary: This is part of a complex and broad relationship that we have the Egyptians -- with the Egyptians. That review that the president ordered in early July has not concluded, and reports to the contrary that reports -- published reports to the contrary that suggest that assistance to Egypt has been cut off are not accurate.
MARGARET WARNER: But Leahy's office stood by its claim, in a statement saying: "The State Department and Foreign Operations Appropriations Subcommittee was told that the transfer of military aid was stopped, that this is current practice, not necessarily official policy, and there is no indication of how long it will last."
Meanwhile administration Cabinet members met at the White House this afternoon to discuss the Egypt aid question further.