An army statement said: "Intelligence resources revealed the killing of [between] 40 and 50 militants."
Officials also said that two Uzbek "extremist fighters" were shot and killed by pro-government tribesman.
The deaths occurred early on Sunday in South Waziristan.
The Pakistani government has attempted to encourage tribes to fight against what they see as undesirable groups - many of whom harbour foreign fighters.
The border with Afghanistan became a scene of constant battles after the September 11, 2001, attacks and Pakistan's consequent support for America's "war on terror".
Earlier, Pakistani officials said 59 fighters were arrested by security forces on Saturday for attacking police with rockets.
Intelligence officials also said that six Pakistani fighters arrested last month were "brainwashed" by extremist clerics and had been planning suicide attacks on military targets.
The men were arrested in December in raids in parts of eastern Punjab province.
On Thursday 19 people were killed by a suicide bomb attack near the high court in Lahore.