Libyan Prime Minister Ali Zeidan has been kidnapped from a hotel in Tripoli by an armed group and taken to an unknown location, the government has said.

A former Libyan rebel group said on Thursday it had "arrested" Zeidan after the government allowed the United States to capture a top al-Qaeda suspect, Abu Anas al-Liby, in Tripoli last weekend.

The Libyan Revolutionary Operations Chamber said on Facebook it had seized the prime minister "on the prosecutor's orders," adding that Zeidan "was arrested under the Libyan penal code... on the instructions of the public prosecutor".

The group said it was on high alert "in light of the deterioration in security and damage to the country's sovereignty by foreign intelligence bodies".

"His arrest comes after the statement by John Kerry about the capture of Abu Anas al-Liby, after he said the Libyan government was aware of the operation," a spokesman for the group said, referring to the US Secretary of State.

Zeidan is in "good health and will be treated well as a Libyan citizen," and is being held at the Interior Ministry's anti-crime department, an official with the department told the state news agency.

Hours before the abduction, Zeidan met al-Liby's family to express his concern about the US raid, AP press agency reported.

Al Jazeera's Mahmoud Abdelwahed, reporting from Tripoli, said the cabinet gathered in an emergency session to discuss the crisis.

"The rebels said they have taken this step by the virtue of a memo by the general prosecution office, but the justice ministry denies such memo was issued," Abdal Wahid said.

The government in a statement said it believed the Revolutionary Operations Chamber was involved but also accused another group, the Brigade for the Fight against Crime, of being behind the kidnapping.

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.

Amel Jerary, the director of communications to the prime minister, told Al Jazeera that the raid happened in the middle of the night. "I'm afraid at this point, nothing is very clear. How it is done, I really don't have any information on this. I'm sure that the people who have done this were very well prepared," Jerary said.

Jerary denied rumours that Libya's finance minister was also kidnapped. "This is not true," she said.

Zeidan was taken by force by gunmen from the Corinthia Hotel in the capital where he resides, security guards at the hotel said.The circumstances were unclear but one guard described it as an "arrest".

Zeidan, who was named prime minister a year ago, had on Tuesday condemned the US raid and insisted that all Libyans should be tried on home soil.

The General National Congress has demanded that Washington "immediately" hand back al-Liby, claiming his capture was a flagrant violation of the country's sovereignty.

Al-Liby, whose real name is Nazih Abdul Hamed al-Raghie, was on the FBI's most wanted list with a $5 million (3.7 million euro) bounty on his head for his alleged role in the 1998 twin bombings of two US embassies in East Africa.

He is reportedly being held aboard a US Navy ship in the Mediterranean.

US President Barack Obama said on Tuesday Liby was involved in plots that killed hundreds of people and would be brought to justice.

Many Libyans blame political rivalries for the problems plaguing a country awash with armed groups and weaponry left over from the 2011 revolution that toppled Muammar Gaddafi.

Public anger is growing as widespread violence including political assassinations proliferates - particularly in the east of the country.