Naamen Maziche of French origin, who was described by the state-run media as a "prominent operative of Al Qaeda responsible for external operations", was captured in a raid near the border with Iran, officials said without disclosing when the incident had taken place.
Maziche, CNN reported had been found to have links with Mohammad Atta, who piloted an American flight into the World Trade Centre on September 11, 2001.
The French Qaeda operative, Pakistani officials said was detained following disclosures by Younis al-Mauritani, another top Al Qaeda militant captured last year.
Al-Mauritani had been appointed by Osama bin Laden as commander of operations in Africa. He was on a list of "most wanted persons".
Some media reports described Maziche as an Al Qaeda operative with links to European jihadi groups.
Al-Mauritan and three of his associates were arrested by Pakistani security agencies in the southwestern city of Quetta last year.
After al-Mauritani's arrest, Maziche moved to Iran, the reports said.
Al-Mauritani had reportedly told interrogators that Maziche had moved to Iran with some of his associates en route to Africa.
Pakistani agencies are now interrogating Maziche.
