"I have made it clear that the United States has a profound respect for people of all faiths," Obama said in his weekly radio address. "Yet there is never any justification for violence .... There is no excuse for attacks on our embassies and consulates."
Angry anti-American protests have swept the Muslim world in response to a film that insults the Prophet Mohammad. An attack on the U.S. consulate in the Libyan city of Benghazi killed U.S. Ambassador Christopher Stevens and three others this week.
A day after Obama led a somber ceremony marking the return of the bodies of the Americans killed in Libya, Obama acknowledged that a surge of anti-American violence in the Middle East is disturbing.
The Pentagon is sending Marines to beef up security at the U.S. embassy in Sudan, following similar reinforcements to Libya and Yemen.
The Libyan attack and the U.S.-directed outrage have raised questions about Obama's handling of the so-called Arab Spring, a series of revolutions that have unseated entrenched authoritarian governments.
The turbulence in the Middle East has had ripples in a tight U.S. presidential election, with Obama's Republican challenger Mitt Romney saying Obama has weakened U.S. authority around the world.
However, Obama repeated a vow to bring the attackers of the U.S. consulate in Libya to justice. "We will not waver in their pursuit," he said.
The president also said the turmoil should not deter U.S. efforts to support democracy in the region or elsewhere.
"Let us never forget that for every angry mob, there are millions who yearn for the freedom, and dignity, and hope that our flag represents," he said. - AGENCIES