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CAIRO — Libya’s prime minister, Ali Zeidan, was briefly kidnapped from a Tripoli hotel Thursday in an apparent act of retaliation for his supposed consent to the capture of a suspected al-Qaida leader by American Special Forces.

He was seized before dawn and freed by early afternoon, according to Amal al Jarrari, a spokeswoman for the prime minister’s office, who could not immediately provide details.

The short-lived kidnapping was an ominous sign for the stability of Libya’s transitional government and its cooperation with American counterterrorist efforts. Zeidan’s abductors appeared to be among the semiautonomous militias who serve as his government’s primary police and security force, according to a statements from the prime minister’s office and a coalition of militia leaders.

A spokesman for the coalition, which calls it the Operations Room of Libya’s Revolutionaries, said the prime minister’s “arrest” followed a statement by Secretary of State John Kerry that “the Libyan government was aware of the operation” that captured the al-Qaida leader, Reuters reported.

The prime minister’s kidnapping was the most serious blow yet to the credibility of Libya’s fragile transitional government. And it also could be a grave setback for U.S. efforts to hunt down other terrorist suspects believed to be at large on Libyan soil, including those suspected of a role in the attack last year on the U.S. diplomatic mission in Benghazi that killed Ambassador J. Christopher Stevens and three other Americans.

Zeidan’s government had said it had no warning or knowledge of the U.S. commando raid last Saturday in which Nazih Abdul-Hamed al-Ruqai, the suspected al-Qaida leader, was captured. In a statement, the government demanded an explanation for what it called “the kidnapping of a Libyan citizen” on the streets of the capital.

At a news conference Tuesday, Justice Minister Salah al-Maghrani appeared shocked: “The news itself was definitely a surprise,” he said. “And having seen the prime minister the same night, I have not seen someone more surprised than the Prime Minister Ali Zeidan.”

But U.S. officials, speaking anonymously, said Zeidan’s government had secretly authorized the arrest and possibly others. Members of the Libyan Parliament had vowed to remove him from office if evidence emerged that he knew in advance.

The kidnapping Thursday was the most ominous sign yet that Libya is sliding toward anarchy two years after the revolution that ended Col. Moammar Gadhafi’s four decades of dictatorship. And it may also serve as a warning to other Libyan officials who contemplate collaborating with the U.S. in its pursuit of alleged terrorists.