Clashes in Libya's second city Benghazi killed at least one soldier after the son of the army's special forces commander there was kidnapped Thursday, a military source and witnesses said.

Medical sources said at least one member of the special forces was killed and two of his colleagues were wounded.

The clashes broke out as heavily armed special forces troops backed by helicopters tracked the abductors of student Ali Abu Khamada, son of their commander Wanis Abu Khamada, after he was "kidnapped by unknown persons near Gar Younes university", a military source said.

Fighting broke out in the Gwarsha, Gar Younes and Al-Hawari districts where several military facilities are in the hands of militias made up of former rebels, the source said on condition of anonymity.

Witnesses said the heaviest clashes were at a base operated by an Islamist ex-rebel group, the Brigade of the February 17 Martyrs.

The group denied on its Facebook page that it had kidnapped Abu Khamada, but also called on all of its members "to return immediately to the brigade".

Special forces members are a frequent target of attack and assassinations in violence-ridden Benghazi, cradle of the 2011 uprising which toppled Moamer Kadhafi.

A military source in Benghazi said Thursday's abduction was aimed at pressuring the special forces to bring about the release of prisoners held by the army.

In late November, several people were killed in three days of clashes between special forces led by Wanis Abu Khamada and the jihadist group Ansar al-Sharia.

And special forces announced last Friday the arrest of four suspects in Benghazi in possession of a hit list of officers to be targeted or who had already been killed. A soldier died in the arrest operation.

Militants have also attacked foreign missions in Benghazi, including a September 2012 assault on the US consulate that killed the ambassador and three other Americans.

Eastern Libya has become a bastion of Islamist extremists, with authorities avoiding a full-blown confrontation with heavily armed former rebels pending the formation of a regular army and police force.