The warrant, first issued in 2013 by the International Criminal Court (ICC), charges Al-Tuhamy Mohamed Khaled, once head of Libya's internal security agency, with three charges of war crimes and four crimes against humanity.
The announcement comes as the court is still in a legal tug-of-war with Libyan authorities to transfer Gaddafi's jailed son Seif al-Islam to the tribunal in The Hague to face trial for crimes against humanity.
The warrant against Khaled says that between February and August 2011, the military, intelligence and security agencies carried out attacks on the civilian population "in furtherance of a policy designed by the Libyan state to quash the political opposition to the Gaddafi regime by any means".
That included "lethal force and by arresting, detaining, torturing and abusing perceived political opponents."
Prisoners across Libya "were subjected to various forms of mistreatment, including severe beatings, electrocution, acts of sexual violence and rape, solitary confinement" as well as mock executions.
As head of the agency from February to August 2011, Khaled "had the authority to implement Gaddafi's orders," it added.
The prosecutor's office asked for the warrant to be made public as it "may facilitate (his) arrest and surrender as all states will then be aware of its existence," the court said.
Born in the Janzour area of Libya, west of Tripoli, in 1942, Khaled was known by several aliases, and had "at least 10 different passports, some issued under other identities," the warrant says.
According to Libyan media, he was arrested in Cairo in April 2012, but was released again as there was no warrant against him. Since then he is believed to have dropped out of sight.
The warrant appeals to the authorities in Egypt to co-operate with the court's request for his arrest and surrender.
Although Libya is not a party to the Rome Statute which underpins the ICC, the U.N. Security Council unanimously mandated the tribunal to investigate abuses in the country in February 2011.
It was then still under the rule of longtime leader Gaddafi, who was killed months later by rebels in a NATO-backed uprising.
- No-one in the dock -
An arrest warrant for alleged crimes against humanity issued in June 2011 is still outstanding for his son, Seif al-Islam, said to be behind bars in Zintan, a town southwest of Tripoli that opposes the unity government based in the capital.
The new unity U.N.-backed government in Tripoli still faces dogged resistance from jihadist holdouts, as well as a rival administration in the east.
A bid by chief prosecutor Fatou Bensouda to have the ICC warrant served on the battalion commander in charge in Zintan, to compel him to turn over Islam to the court, was turned down by the trial chamber in November.
So far no-one has stood trial for atrocities in Libya, as the case against Gaddafii's former intelligence chief Abdullah Al-Senussi was dropped, after it was declared inadmissible in October 2013.
But Bensouda has vowed her office would keep up its investigations, and said last year new arrest warrants could perhaps follow in 2017.
She vowed to make Libya a priority for her office, and told the U.N. Security Council in November she would seek to expand investigations to "potentially include alleged crimes committed by Daesh.
It would be the first such moves by the court -- set up in The Hague in 2002 to try the world's worst crimes -- to target Daesh jihadists who swept to power across a swathe of Iraq and Syria in 2014.
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