"I now call on the Egyptian military to move quickly and responsibly to return full authority back to a democratically elected civilian government as soon as possible through an inclusive and transparent process, and to avoid any arbitrary arrests of President Morsi and his supporters," Obama said.
The U.S. wasn't taking sides in the conflict, committing itself only to democracy and respect for the rule of law, Obama said.
Hours earlier, Egyptian armed forces ousted Morsi, an Islamist and Egypt's first democratically elected president, after just a year in power. The military installed a temporary civilian government, suspended the constitution and called for new elections.
Morsi denounced his ouster as a "full coup" as millions of his critics erupted in delirious scenes of joy in Egyptian cities after the army chief made the announcement on television.
Obama huddled in the White House Situation Room on Wednesday afternoon with Defense Secretary Chuck Hagel, Attorney General Eric Holder and his new national security adviser, former U.N. Ambassador Susan Rice. In his statement after the meeting, Obama said he expected the military to protect the rights of Egypt's men and women to due process and peaceful assembly. He reaffirmed his call for a democratic Egypt that involves participation from secular and religious parties alike.
"The voices of all those who have protested peacefully must be heard, including those who welcomed today's developments, and those who have supported President Morsi," Obama said, urging all sides to refrain from violence.
Egyptian military leaders have assured the Obama administration that they were not interested in long-term rule following their toppling of Morsi. They appointed a government of civilian technocrats to temporarily run the country in an apparent bid to forestall potential U.S. sanctions, American officials said Wednesday.
If it is deemed that any country's democratically elected leader is deposed by the military, the U.S. must cut off aid. But the administration can take time to make the legal determination about whether Morsi's ouster constituted a coup, and Obama appeared Wednesday to be treading cautiously.
But on Capitol Hill, some lawmakers were preparing next steps. Sen. Patrick Leahy, who heads the Appropriations panel that oversees foreign aid, said he hoped Egypt's military would make good on its vow to return power to the people, but that in the meantime, U.S. law was clear about what should happen.
"My committee also will review future aid to the Egyptian government as we wait for a clearer picture," said Leahy, D-Vt.
In conversations with Hagel and Gen. Martin Dempsey, chairman of the Joint Chiefs of Staff, senior Egyptian army officers pledged to put a civilian government in place quickly if not immediately after removing Morsi from power, the U.S. officials said. The officials spoke on condition of anonymity because they were not authorized to speak by name about the private conversations that occurred over the past week.
The officials also said the Egyptian military pledged to take steps to ensure the safety of Americans in Egypt, including the embassy in Cairo and the consulate in Alexandria. One official said the State Department was ordering all nonessential U.S. diplomats and the families of all American embassy personnel to leave Egypt.
The State Department earlier Wednesday said it had been disappointed with Morsi's response to opposition protesters demanding his ouster, saying the Muslim Brotherhood leader had not presented any plans to address their legitimate concerns when he addressed the nation in a televised speech late Tuesday.
"Last night was an opportunity for him to propose new steps, which he ... did not," State Department spokeswoman Jen Psaki said.