The commander of a powerful Libyan militia said Monday that looters had stolen “a large number” of shoulder-fired, heat-seeking missiles from the militia’s base when protesters who called for dismantling the country’s militias overran the compound.

Ismail Salabi, the commander of Rafallah al-Sahati, a powerful Islamist militia in Benghazi, said in an interview that the missiles, used by fighters to “hit airplanes” and known to the U.S. intelligence community as MANPADS (man-portable air-defense systems), were stolen along with 2,000 semiautomatic rifles and ammunition, as the militia withdrew from its base amid a firefight early Saturday.

Saleh Jouda, a member of Libya’s elected General National Congress and the deputy head of national security, said the government did not have any information about stolen weapons aside from “between 1,000 and 2,000 guns.” He said the government had set up new security checkpoints to track down the weapons. But there was no evidence of new checkpoints in Benghazi on Monday.

The militias were carrying out arrests Monday of people believed to have been involved in the weekend incidents.

The clashes at Rafallah al-Sahati’s base followed a mass protest Friday, during which thousands of Libyans marched through Benghazi demanding the establishment of a strong national army and the dissolution of the hundreds of militias that have run Libya’s streets in the security vacuum since Moammar Gaddafi’s fall last year.

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By early Saturday, protesters, aided by other government-allied militias, had overrun four militia bases, including Rafallah al-Sahati’s, and a base belonging to the extremist group Ansar al-Sharia, which many here have accused of involvement in the Sept. 11 attack on the U.S. Consulate that killed the U.S. ambassador and three other Americans.

Libya’s militias consist largely of former rebels who in some cases have amassed large quantities of heavy weapons, stolen from Gaddafi’s arsenals over the course of Libya’s eight-month revolution. The country’s weak central government has yet to develop a clear plan to collect those weapons.

The president of the General National Congress told reporters Saturday that all of the militias would be absorbed into a unified national force, or required to disband. However, there is a fine line between the militias that already fall under the loose central command in Tripoli and those that don’t.

During Monday’s interview, Salabi referred to his militia at times as “the nucleus of the new Libyan army,” and at other times as an organization separate from and victimized by the national army. He also said that his group and two other government-affiliated militias are the only groups in Benghazi capable of reclaiming the stolen weapons.

“There is no organized militia that can get these weapons back, other than Rafallah al-Sahati, the February 17th [Brigade] and Libya Shield. We can attack the places where the weapons are,” he said.

It was unclear whose hands the weapons had fallen into. But Salabi suggested that clashes had broken out between rival militias over the looting of Rafallah al-Sahati’s weapons. “Most of the clashes were over who was going to get control of the weapons,” he said.

A senior Obama administration official said earlier this month that U.S. intelligence estimates that 100 to 1,000 MANPADS are still unaccounted for in Libya, despite U.S. efforts to destroy them. Intelligence officials believe that some of the MANPADS have been smuggled across Libya’s borders.

Glen Doherty, a former Navy SEAL and one of the Americans killed in the consulate attack, told ABC News last month that he had gone into Libya to track down MANPADS as a contractor for the State Department.

The United States and the Soviet Union stockpiled MANPADS during the Cold War. Although military aircraft now have countermeasures that have rendered the weapons largely ineffective in conventional battle, MANPADS continue to pose a serious threat to passenger planes.

Under Gaddafi’s rule, Libya is believed to have collected more MANPADS than any other nation that did not produce them, according to the State Department. During the country’s 2011 civil war, rebels seized troves of weapons from government depots. Many were later sold on the black market. Fearing that terrorist groups could acquire Libyan MANPADS, U.S. officials in November launched a $40 million effort to recover the missiles.

“In the wrong hands, shoulder-fired antiaircraft missiles pose a major threat to passenger air travel, the commercial aviation industry and possibly military aircraft around the world,” Andrew J. Shapiro, an assistant secretary of state who oversees the effort said in a speech this year. “Not only could a successful attack against an aircraft cause a devastating loss of life, but it could also cause significant economic damage.”

Meeting with Libya’s president on the sidelines of the U.N. General Assembly on Monday, Secretary of State Hillary Rodham Clinton gave a strong endorsement of Libya’s democratic transition. She did not mention the Benghazi consulate attack during brief opening remarks heard by reporters.

Libyan President Mohamed Yusuf al-Magariaf thanked Clinton for U.S. support and said Libya bears “a grave responsibility for this tragedy.” He pledged to “expedite the investigation in the incident and to bring to justice the perpetrators.”

Magariaf noted that thousands of Libyans had marched in the streets to protest the attack. Those demonstrations “embodied the conscience of the Libyan people,” he said.

“What happened on [the] 11th of September toward these U.S. citizens does not express in any way the conscience of the Libyan people, their aspirations, their hopes or their sentiments toward the American people,” he said.

Earlier Monday, Clinton addressed the wave of often violent anti-American protests related to a YouTube video that mocks Islam.

“Dignity does not come from avenging insults, especially with violence that can never be justified,” she said in remarks to her husband’s Clinton Global Initiative development forum. “It comes from taking responsibility and advancing our common humanity.”

Anne Gearan in New York and Ernesto Londoño in Washington contributed to this report.