The pre-dawn abduction comes five days after US commandos embarrassed and angered Libya's government by capturing senior Al-Qaeda suspect Abu Anas al-Libi off the streets of Tripoli and whisking him away to a warship.
"The head of the transitional government, Ali Zeidan, was taken to an unknown destination for unknown reasons by a group" of men believed to be former rebels, the government said in a brief statement on its website.
"A large number of armed men entered the place very early on Thursday. But we did not know what was happening," a hotel employee told AFP, speaking on condition of anonymity.
A group of former rebels, which had roundly denounced Libi's abduction and blamed Zeidan's government for it, said it had "arrested" Zeidan.
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The Operations Cell of Libyan Revolutionaries, which in principle reports to the defence and interior ministries, said on Facebook it had seized Zeidan "on the prosecutor's orders".
The premier "was arrested under the Libyan penal code... on the instructions of the public prosecutor", the group said. It said he was detained for "crimes and offences prejudicial to the state" and its security.
The Operations Cell of Libyan Revolutionaries had expressed outrage at the brazen daylight raid by US commandos to capture Libi. It said on Tuesday it had told its fighters to be prepared for orders to "hunt down and expel foreigners who are illegally in the country".
Today's government statement said it suspected two groups of ex-rebels, the Operations Cell of Libyan Revolutionaries and the Brigade for the Fight against Crime, of being behind the abduction.
The cabinet and the General National Congress, Libya's top political authority, were dealing with the situation, the statement said, while calling on citizens to remain calm.