The group suspected of carrying out the consulate attack is called Ansar al Sharia, according to Libyan sources. But the group, which is close to al Qaeda in ideology and is based in east Libya, has denied responsibility for the attack.
Libyan President Mohammed Yussef Magariaf promised to coordinate additional support to protect Americans in the country, condemned the assault on the embassy and pledged his government's full cooperation, Clinton said.
Mohammed el-Megarif, Libya's interim president, apologized to the U.S. on Wednesday for the attack that killed Stevens and vowed to bring the culprits to justice.
Stevens, who was a career member of the Senior Foreign Service and served two tours of duty in Libya, began his term of appointment on May 22, and he was in Libya during the uprising that deposed Qaddafi, serving as the American representative to the transitional national council.
A senior U.S. official told ABC News the State Department is on alert throughout the region and fears there could be more attacks to come.
In Cairo, protesters enraged by the movie scaled the embassy walls and took down the flag from a pole in the courtyard. After trying unsuccessfully to burn it, they ripped it apart and replaced it with a black flag bearing Arabic writing.
The movie was made by Israeli producer Sam Bacile, according to a statement released Wednesday from Afghanistan President Hamid Karzai, and has been promoted by controversial pastor Terry Jones, the Florida preacher whose Koran burning in March 2010 led to the deadly violence in Afghanistan.
Jones said Tuesday in a statement that the movie was titled "Innocence of Muslims" and was intended not to attack Muslims but to show the "destructive ideology of Islam."
"The movie further reveals in a satirical fashion the life of Muhammad," he said.
Afghan President Hamid Karzai issued a statement condemning the movie and called it an "insult" to Islam.
"Desecration is not a part of the freedom of expression, but a criminal act that has now badly affected the righteous sentiments of 1.5 billion Muslims all over the globe," Karzai said.
ABC News' Martha Raddatz and The Associated Press contributed to this report.