Under US law, the government must suspend foreign aid to any nation whose elected leader is ousted in a coup d'etat.
The US provides $1.5 billion a year to Egypt in military and economic assistance that is considered a critical US national security priority.
"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 US wasn't taking sides in the conflict, committing itself only to democracy and respect for the rule of law, Obama claimed.
With the threat of further unrest roiling Egypt, the State Department ordered all nonessential US diplomats and the families of all American embassy personnel to leave the country.
Hours earlier, Egyptian armed forces ousted Morsi and 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 UN Ambassador Susan Rice.