The troops disappeared after militants attacked security posts and a foot patrol near the town of Mir Ali in the North Waziristan region, an army statement said.
The fighting came as one of three helicopters escorting President Gen. Pervez Musharraf crashed in Pakistan's portion of Kashmir, killing four passengers and injuring five, officials said. The president was unhurt.
Maj. Gen. Waheed Arshad, an army spokesman, blamed a "technical fault" for the crash of the military helicopter and said Musharraf had already reached his destination when the accident occurred.
The crash revived concerns about the safety of the U.S.-allied general who has survived several assassination attempts. It happened two days after he secured ain a controversial presidential election.
Musharraf traveled to Kashmir on Monday to commemorate the second anniversary of the Oct. 8, 2005, earthquake that killed nearly 80,000 people. The helicopter crashed in Mujhoi, about 12 miles south of Muzaffarabad, the main town in Pakistan's portion of the disputed Himalayan territory.
Arshad said the dead included an army brigadier, two soldiers and a cameraman for Pakistan Television. Two pilots and a technician escaped unhurt, he said.
Witnesses said the helicopter's engine was on fire before it hit the ground but there was no indication it had come under attack. Minutes before, two other helicopters flew past the village, they said.
Naseer Ahmed, a resident, said the noise of the engine suddenly grew louder and the pilots found level terrain on the outskirts of the village for an emergency landing. He said several passengers jumped from the chopper before it hit the ground and exploded.
The helicopter was one of three taking Musharraf and others to Muzaffarabad for quake commemorations, said a senior army official speaking on condition of anonymity because was not authorized to comment to media.
Arshad said only that an army helicopter made a crash landing in the Jhelum Valley due to a technical fault while en route to Muzaffarabad. He declined to say how close Musharraf had been to the crash.
"The president was in some other chopper and he safely reached where he had to go," he said.
Monday's fighting in Waziristan coincides with a change of command in the Pakistani army, which is suffering heavy losses in an escalating confrontation with militants who have seized control of swaths of territory near the frontier.
The army said earlier that about 60 suspected militants and 20 soldiers had died in two major clashes in North Waziristan on Sunday.
A security official in Miran Shah, the region's main town, said army helicopters and jets bombarded militant positions in several villages in the region.
He said informers had told security forces that two Arabs who were low-ranking al-Qaida men and an Uzbek died in the second battle in an area called Malagam.
About a dozen civilians, including women and children, died when a stray mortar struck their home in Mir Ali, said the official, who spoke on condition of anonymity because he was not authorized to speak to the media. It was unclear who fired the mortar.
Asked about reported civilian deaths on Geo television on Monday, army spokesman Maj. Gen. Waheed Arshad said security forces had fired only at targets from which they were being attacked.