The missing soldiers have been out of radio contact since the morning in North Waziristan.
"There has been no contact with about 40 to 50 soldiers since then. We are trying to find out where are they," said Major-General Waheed Arshad, a military spokesman.
The news comes as a fresh blow to the army, with fighters already holding more than 200 Pakistani soldiers in neighbouring South Waziristan since the end of August.
Pakistani troops backed by helicopter gunships had launched an assault overnight on Friday against fighters based in the region after several military convoys were attacked, with more than 80 people killed in the battle.
"Sixty militants have been killed by security forces in North Waziristan Agency since Sunday morning," an army statement said on Monday.
The statement also said that 20 members of the security forces had also been killed.
Residents said four civilians also died, including three women, although the military could not confirm this.
Surge in violence
Many in Waziristan support the Taliban and al-Qaeda members, who fled to the region after US-led forces drove them out of Afghanistan in late 2001.
There has been a rise in fighting since July when tribal groups scrapped a peace deal with the authorities in North Waziristan and army commandos stormed a mosque and religious school in Islamabad, Pakistan's capital.
Pervez Musharraf, the president who was again elected in a vote on Saturday, has said "terrorism" is one of the biggest challenges to the country.
But the conflict has reinforced opposition among many Pakistanis, mainly in the conservative northwest, to Musharraf over his support for the US's so-called "war on terror".