Elsewhere in the northwest, a suspected U.S. missile killed 14 people, but apparently missed a top Taliban figure, authorities said.
Pakistan's 8-day-old offensive in the Taliban and al-Qaida stronghold of South Waziristan is considered its most critical test yet in the campaign to stop the spread of violent extremism in this nuclear-armed country. The army operation has prompted a wave of retaliatory attacks by militants this month that have killed some 200 people.
The battle for Kotkai town took days, and involved aerial bombardment as soldiers captured heights around the town. The final fight killed 13 militants and two soldiers, said an army officer and an intelligence official. The military has begun to clear the town of land mines and roadside bombs planted by the insurgents.
The officials spoke on condition of anonymity because they were not authorized to speak to media on the record.
Kotkai is symbolically important because it is the hometown of Pakistani Taliban chief Hakimullah Mehsud and one of his top deputies, Qari Hussain. It also lies along the way to the major militant base of Sararogha, making it a strategically helpful catch.
South Waziristan is part of Pakistan's semi-autonomous tribal belt, a rugged stretch of land along the Afghan frontier where al-Qaida chief Osama bin Laden is rumored to be hiding. Pakistan is under intense international pressure to clear its tribal areas of insurgents, many of whom are blamed for attacks on U.S. and NATO troops in Afghanistan.
The U.S. has launched scores of missile strikes in the region over the past year, killing several top militants including former Pakistani Taliban chief Baitullah Mehsud.
The latest strike hit Chuhatra village in the tribal region of Bajur, local government official Mohammad Jamil said.
The missile hit a hide-out of the militants that included a tunnel, Jamil said. The target appeared to be Faqir Mohammad, a prominent Taliban leader, but he is believed to have escaped, Jamil said.
Pakistan formally protests the strikes, saying they violate its sovereignty and raise sympathy for the Taliban, while the U.S. rarely discusses the attacks. Analysts believe the two sides have a secret deal allowing the strikes.