Officials on Saturday said they suspected fighters to be hiding in the tribal area bordering Afghanistan.
Severe economic penalties had also been imposed on the tribe, which last month formed a 1200-strong tribal force to capture the foreign fighters and avoid further military action.
"We have arrested 13 leaders of Wazir tribes because their Lashkar (tribal force) failed to arrest foreign suspects hiding in the area," local official Ismat Allah Gundapur told reporters.
The action came a week after Pakistan's top military officials warned that suspected al-Qaida-linked fighters in the South Waziristan area would have to surrender or face "elimination".
'Consequences and repercussions'
The high level meeting was chaired by army chief and president General Pervez Musharraf. The meeting warned that tribesmen protecting the fighters "will be dealt with severely."
Authorities have been making efforts to persuade the fighters, believed to number between 300 and 600, to surrender and register after the army called off a 12-day offensive against them in late March.
But the fighters, mainly Chechens and Arabs with some Chinese among them, have so far defied orders to undergo a registration process that would involve photographic identification.