"No one kidnapped him," the LANA news agency quoted the official as saying.
Information came in earlier that unidentified armed men forced their way into Tripoli's Corinthia Hotel which houses the residence of the Head of Cabinet and, threatening him with weapons, took him away to an unknown destination.
According to the Al-Jazeera television channel, the premier was arrested during a joint operation of the interior ministry and the so-called operations headquarters of some former rebels on instructions of the attorney general.
Charges of corruption and of implication in the arrest of Abu Anas al-Libi, an alleged Al Qaida leader by US special forces in Tripoli Saturday were ostensibly brought against Zeidan, the Sky News-Arabia TV channel reported.
However, the Al-Arabia channel quoted the country's attorney general as saying that he personally "did not issue a warrant" for the arrest of Zeidan.
Cabinet sources officially stated that the premier was kidnapped by "unidentified armed people".
"Zeidan was kidnapped by unidentified armed persons who took him away to an unknown destination," the prime minister's spokesman Mohamed Kaabr said.
In particular, government sources laid the blame for the kidnapping on the rebels of the city of Az Zawiah which is situated on the Mediterranean coast, 50 km from the capital.
Justice Minister Salah Bashir Margani also told Al-Arabia that Zeidan had been kidnapped by armed militants
The Libyan government is holding an urgent meeting following these developments.