Government officials have confirmed that he was snatched from a hotel he was staying at in the capital and taken to an unknown destination.
Guards at the Corinthia Hotel have described the incident, which saw two of Zeidan's guards also taken, as an 'arrest'.
The men that have taken Mr Zeidan are believed to be former rebels.
Two groups are reportedly suspected of the kidnapping, the chamber of revolutionaries and the brigade for the fight against crime, which in principal fall under the defence and interior ministries.
Two years after a revolution toppled Muammar Gaddafi, Libya's central government has been struggling to contain rival tribal militias and Islamist militants who control parts of the country.
On Tuesday, Mr Zeidan called for the West to help stop militancy in his country.
The men are believed to arrived at the hotel in a convoy of vehicles at dawn and led Mr Zeidan out of the hotel.
There is thought to have been no gunfire.
A statement on the Libyan Government's website read: 'The head of the transitional government, Ali Zeidan, was taken to an unknown destination for unknown reasons by a group.'
The kidnap comes after Islamist militant groups were angered last weekend when a top al Qaeda suspect was captured by U.S military in Tripoli.
Libyan militants had vowed revenge for the capture of Abu Anas al-Liby by U.S special forces.
He was seized in an early morning raid over the bombing of U.S embassies in Tanzania and Kenya in 1998.
Extremists took to Facebook to urge fellow Libyans to target ships and planes as well as taking U.S. citizens hostage in order to exchange them for imprisoned jihadists.
The Revolutionaries of Benghazi, Al-Bayda and Derna wrote on Facebook:
"We condemn this act, and pledge before God to fight those who betrayed their country and involved themselves in this plot.
"We also say to the Libyan people that we didn't fight against the dead leader to replace him with a traitor or foreign agent who would deliver up our compatriots out of loyalty to the infidels."
Apparently they made good their promise.
Mr Zeidan's kidnap comes just hours after he met with members of al-Liby's family on Wednesday.
Mr Zeidan was appointed Prime Minister by the General National Congress in Libya in October last year and took office the following month.
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