He was questioned for two hours by anti-terrorist magistrate Marc Trevidic, who is leading an inquiry into the attack that has sparked allegations of political corruption and revenge-taking in France.
Villepin was questioned last Thursday for four hours as a witness in a separate probe into whether French officials received illegal payments related to arms deals in 1995.
Witnesses have alleged the Pakistan bombing was revenge for the cancelling of kickbacks paid to officials in the arms deals, in a complex case linked to alleged illegal political funding and implicating President Nicolas Sarkozy.
But Villepin repeated Tuesday during questioning that he did not believe there was any link between the attack in Karachi and the stopping of the payment of the commissions, the source said.
Villepin was chief of staff to then president Jacques Chirac, who cancelled the commissions after he took office in 1995 because he suspected they would lead to kickbacks to his political rival Edouard Balladur, a Sarkozy ally.
Villepin is also Sarkozy's bitterest political rival and likely to run against him for president in 2012.
Witnesses have also alleged Sarkozy, budget minister at the time of the arms deal and Balladur's campaign spokesman, was linked to the commissions.
The current French leader has angrily dismissed talk of his involvement as a "fairy tale" and denies any knowledge of kickbacks.
The bombing in Karachi in 2002 killed 11 French engineers and at least three Pakistanis. Relatives of the French victims plan to sue Villepin and Chirac for manslaughter and have called for Sarkozy to testify.
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