Gunmen from a former rebel faction seized Libyan Prime Minister Ali Zeidan from a Tripoli hotel on Thursday, the government said.
"The head of the government Ali Zeidan was taken at dawn this morning by gunmen to an unknown place for unknown reasons," the statement said.
Guards at the Corinthia Hotel said gunmen had taken Zeidan from the hotel but there were no shots fired or clashes during the incident.
One guard described it as an "arrest" while another told Reuters the men were militants.
Government officials could not immediately be reached to give more details.
Al Arabiya television channel quoted Libya's justice minister as saying that Zeidan had been "kidnapped" and showed what it said were video stills of Zeidan frowning and wearing a grey shirt undone at the collar surrounded by several men in civilian clothes pressing closely around him.
Two years after a revolution toppled Libya's Col. Muammar Gaddafi, the fragile central government has been struggling to contain rival tribal militias and Islamist militants who control parts of the country.
Last weekend, the US military captured a top Al Qaeda suspect in Tripoli in a raid that angered Islamist militant groups, including one blamed for the 2012 attack on the U.S. consulate, in Benghazi.
The US State Department was looking into the reports of the incident and was "in close touch with senior US and Libyan officials on the ground," spokeswoman Jen Psaki said.