The comment appeared to reflect changing assumptions on the Middle East in the US government, which has seen decades-old allies swept away in the Arab Spring to be replaced by less sympathetic but more representative governments.
"The president, in diplomatic and legal terms, was speaking correctly. We do not have an alliance treaty with Egypt. Ally is a legal term of art," White House spokesman Jay Carney said.
"But as the president has said, Egypt is a long-standing and close partner of the United States and we have built on that foundation in supporting Egypt's transition to democracy and working with the new government."
US relations with Egypt, delicate since the fall of former dictator Hosni Mubarak, are coming under fresh scrutiny after a mob stormed the US embassy in Cairo and tore down the US flag.
Obama spoke with President Mohamed Morsi, the first Islamist leader following an uprising which toppled Mubarak last year, on Wednesday and impressed upon him the need to protect US diplomats, Carney said.
Morsi then said Thursday that foreign diplomats in Egypt should be kept safe, but also slammed a US-made amateur movie deemed insulting to Islam which has sparked fury and violence in Egypt, Libya and Yemen.
Obama made his comment in an interview with Spanish-language Telemundo on Wednesday.
"I don't think that we would consider them an ally, but we don't consider them an enemy," the president said.
"I think that we are going to have to see how they respond to this incident," Obama said.
"Certainly in this situation, what we're going to expect is that they are responsive to our insistence that our embassy is protected, our personnel is protected," Obama said.
Egypt, after Israel, is the largest recipient of US foreign aid, and as it seeks to bolster Morsi's effort to consolidate power against a rising challenger for extremists, Washington is weighing a deal with Egypt's new rulers to relieve $1 billion worth of debt.