WASHINGTON — The attack in Benghazi, Libya, that killed Ambassador J. Christopher Stevens and three other Americans has dealt the US Central Intelligence Agency a major setback in its intelligence-gathering efforts at a time of increasing instability in the North African nation.

Among the more than two dozen American personnel evacuated from the city after the assault on the American mission and a nearby annex were about a dozen CIA operatives and contractors, who played a crucial role in conducting surveillance and collecting information on an array of militant armed groups in and around the city.

‘‘It’s a catastrophic intelligence loss,’’ said one US official who has served in Libya and who spoke on the condition of anonymity because the FBI is still investigating the attack. ‘‘We got our eyes poked out.’’

The CIA’s surveillance targets in Benghazi and eastern Libya include Ansar al-Sharia, a militia that some have blamed for the attack, as well as suspected members of Al Qaeda’s affiliate in North Africa, known as Al Qaeda in the Islamic Maghreb.

Eastern Libya is being buffeted by strong crosscurrents that intelligence operatives are trying to monitor closely. The killing of Stevens has ignited public anger against the militias, underscored Friday when thousands of Libyans took to the streets of Benghazi to demand that the groups be disarmed.

‘There was no trust before the election of the National Congress that is backed by the legitimacy of the people and which chose the country’s leader.’

The makeup of militias varies widely; some are moderate, while others are ultraconservative Islamists known as Salafis and still others are loyalists from the government of Moammar Khadafy, the deposed Libyan leader.

‘‘The region’s deeply entrenched Salafi community is undergoing significant upheaval, with debate raging between a current that is amenable to political integration and a more militant strand that opposes democracy,’’ Frederic Wehrey, a senior policy analyst with the Carnegie Endowment for International Peace who closely follows Libya and visited there recently, wrote in a paper this month, ‘‘The Struggle for Security in Eastern Libya.’’

American operatives at the mission also assisted State Department contractors and Libyan officials in tracking shoulder-fired missiles taken from the former arsenals of Khadafy’s forces; they aided in efforts to secure Libya’s chemical weapons stockpiles; and they helped train Libya’s new intelligence service, officials said.

Senior US officials acknowledged the intelligence setback, but insisted that information was still being collected using a variety of informants on the ground, systems that intercept electronic communications like cellphone conversations, and satellite imagery. Spokesmen for the State Department and the White House declined to comment Sunday.

Meanwhile, Liibya’s interim government on Sunday ordered the breakup of all militias that do not fall under its authority, and demanded that those militias pull out of military compounds and public property within 48 hours.

Mohamed al-Magarief, the president of Libya’s national Congress and the interim head of state, apparently sought to both appease public anger and capitalize on it with the order to withdraw and disband. Previous interim leaders have issued similar calls before without success, in part because the Libyan government still depends on many of the self-organized militias to act as its military, police, and national guard.

Hundreds of such armed groups were formed during and after the uprising against Moammar Khadafy, typically armed with Kalashnikov rifles, rocket-propelled grenades, and truck-mounted artillery captured or looted from Khadafy’s armories. Since his overthrow the groups have been both the main guardians of the social order in Libya and the chief menace to it.

As recently as Friday the Libyan army’s chief of staff, Yousef al-Mangoush, urged protesters not to molest the many militias that were now officially authorized and ostensibly operating under the army’s direction, because the government still needed them to control the country.

But it can be difficult to tell which militias are authorized and which are not. The authorized militias usually still report to their original commanders, and those commanders may or may not follow orders from the Defense Ministry or act on their own. The fighters and their commanders may say sometimes that they are part of the Libyan government and other times that they are outside it.

Within months of the start of Libyan revolution in February 2011, the CIA began building a meaningful but covert presence in Benghazi, a locus of the rebel efforts to oust the government of Khadafy.

Though the agency has been cooperating with the new post-Khadafy Libyan intelligence service, the size of the CIA’s presence in Benghazi apparently surprised some Libyan leaders. The deputy prime minister, Mustafa Abushagour, was quoted in The Wall Street Journal last week saying that he learned about some of the delicate American operations in Benghazi only after the attack on the mission, in large part because a surprisingly large number of Americans showed up at the Benghazi airport to be evacuated.

‘'We have no problem with intelligence sharing or gathering, but our sovereignty is also key,’’ said Abushagour.

The attack also raised questions about the adequacy of security preparations at the two US compounds in Benghazi: the US mission, the main diplomatic facility where Stevens and another American diplomat died of smoke inhalation after an initial attack, and an annex a half-mile away that encompassed four buildings inside a low-walled compound.