Barack Obama has said the United States does not currently consider Egypt to be an ally.
The president was speaking with reference to violent clashes at the US embassy in Cairo, over a US-made anti-Islamic film which has sparked anger among Muslims.
Barack Obama’s comments also came after the storming of the US consulate in Benghazi, Libya, which killed the US ambassador on Tuesday.
President Barack Obama referred to US-Egypt relations as a “work in progress”.
“I don’t think we would consider them an ally, but we don’t consider them an enemy. They are a new government that is trying to find its way,” Barack Obama said in a television interview with Spanish-language network Telemundo.
He said that so far Egypt’s government has “said the right thing and taken the right steps” but it has also responded to other events in ways that “may not be aligned with our interests”.
Barack Obama also said that he expected Egypt to protect the US embassy and its staff.
“If they take actions that indicate they are not taking those responsibilities, as all other countries do where we have embassies, I think that’s going to be a problem,” he said.
Egypt was a close and vital Middle East ally of the United States while ousted President Hosni Mubarak was in power.
Cairo has been key US ally since 1979 Egypt-Israel peace deal, and the US gives more than $1 billion in military aid to Egypt every year.
After last year’s uprising and the resurgence of the once-banned Muslim Brotherhood, question marks have been raised over the future of the relationship.
Angry anti-US protests have taken place across the Middle East and North Africa.
The grounds of the US embassy in the Yemeni capital Sanaa were briefly stormed by protesters on Thursday.
On Wednesday, demonstrators in Cairo angry at the film – Innocence of Muslims – breached the walls of the US embassy and tore down the flag. The clashes, which began on Tuesday, continued in the early hours of Thursday morning.
Egypt’s interior ministry says 16 people were injured overnight – 13 of them members of the security forces. Two police vehicles were burnt out and 12 protesters were arrested.
President Mohamed Mursi has appealed for calm: “I call on everyone to take that into consideration, to not violate Egyptian law… to not assault embassies.”
“I condemn and oppose all who… insult our prophet. [But] it is our duty to protect our guests and visitors from abroad,” he said in a statement broadcast by state media.
In July US Secretary of State Hillary Clinton met Mohamed Mursi for the first time and reaffirmed Washington’s “strong support” for the Egyptian people and their shift to civilian rule.