Major-General Shaukat Sultan, a military spokesman, told Reuters on Thursday: "Latest information shows that at least 40 miscreants were killed."
Army sources had earlier put the tally at 16.
Pakistani forces launched a counter-offensive using helicopter gunships on Wednesday after militants killed four paramilitary troops in an attack on their post in the Shawal area of North Waziristan.
Shawal is about 50km west of North Waziristan's main town of Miranshah.
A statement from the administration of tribal affairs in North West Frontier Province said 19 militants were arrested and they all came from North and South Waziristan.
It said about 150 militants were involved in the fighting.
Tensions have been running high in North Waziristan since last month's clashes in which around 200 tribesmen were killed.
Call to arms
Musharraf has told foreign
fighters to leave Pakistan
The tribesmen were answering a call to arms by militant Muslim clerics after a special forces attack on an al-Qaeda camp.
Pervez Musharraf, the Pakistani president and a key ally in the US-led war on terrorism, warned foreign militants hiding in the tribal region last month to leave Pakistan or be killed.
Many al-Qaeda and Taliban fighters fled to Pakistan's semi-autonomous tribal belt after US-led forces toppled the Taliban regime in Afghanistan.
Osama bin Laden, the al-Qaeda chief, and his deputy, Ayman al-Zawahri, are thought to be hiding in the border region between Pakistan and Afghanistan.