Pakistani tribal sources told Aljazeera that the militants kidnapped nine soldiers.
The administrator of the region, Syed Zaheerul Islam, said the fighters had entered Pakistan's North Waziristan tribal region after a raid inside Afghanistan. Army troops and three helicopter gunships attacked them.
Islam said: "They were foreigners. They had set up tents in mountains in the area."
Islam said they were running a training camp and that the strike triggered explosions in an arms dump at the site.
Major-General Shaukat Sultan, the Pakistani army spokesman, said the early morning operation took place near Saidgi, a village about 15km west of Miran Shah, the main town in North Waziristan.
Special task force
Sultan said the raid was carried out on "confirmed intelligence" that the fighters were in the area.
He did not have information on any casualties, saying troops from a special operation task force had cordoned off the scene of the raid, and were carrying out a search.
Last month, Pakistan protested to the US military in Afghanistan over firing that hit the same village killing eight people.
The latest attack came shortly after 7am (0200 GMT), three days before George Bush, the US president, is due to arrive in Pakistan.
The region of the attack is now under curfew.