An intelligence official, however, said on Sunday that hundreds of civilians were fleeing the embattled towns in North Waziristan.
Earlier during the day, helicopter gunships backed ground troops in the intermittent clashes in Miran Shah, the main town in the North Waziristan tribal region.
The fighting came just days after the army attacked a suspected al-Qaida camp in the village of Saidgi near the Afghan border. Military officials said 45 people, including foreign militants, were killed in the attack.
But the tribesmen - who sympathise with the militants - claim local people died and the operation whipped up more anti-government anger in the area - about 190km from Peshawar, the provincial capital.
Saturday's fighting took place about 300km southwest of Islamabad, where George Bush, the US president, made a 24-hour visit and declared his solidarity with Pakistan in the war on terror.
Major General Shaukat Sultan, the army spokesman, said 25 militants were killed in Miran Shah and 21 in Mir Ali, but added that the toll could be higher than that.
Pakistan has deployed about 80,000 forces along the Afghan frontier, but has failed to assert the government's control in these tribal regions which have resisted outside influence for centuries.
Waziristan is known as a hotbed of al-Qaida and Taliban militants who draw support from the local Pashtun tribal people.
Many of the rebellious tribesmen involved in Saturday's unrest are believed to be Islamic students, referred to as "local Taliban" - reflecting their sympathies with the hardline militia in Afghanistan.
Anger has been stirring among the tribesmen since Pakistan's army attacked the suspected al-Qaida camp earlier this week in Saidgi.
Saturday's fighting began in the town of Mir Ali, when tribesmen opened fire on vehicles carrying paramilitary rangers, said an army officer.
It then spread to nearby Miran Shah. About 500 armed tribesmen traded fire with paramilitary forces and, according to security officials, occupied government buildings. A witness said both sides using mortar shells and assault rifles. Some shells hit closed shops.
Soon after the clashes started, phone lines to the town went dead.