The troops backed by helicopter gun-ships on Saturday killed at least 46 tribal militants in clashes with insurgents angry at an earlier raid on their hideout in Saidgai village, officials said.
Three soldiers were also killed as fierce fighting was still raging in North Waziristan tribal region bordering Afghanistan.
Hundreds of terrified residents fled the area before the clashes started and all roads were closed, officials and local sources said.
Around 25 died in Mir Ali, a town in the North Waziristan tribal region, while another 21 were killed in another location near the area's main town of Miranshah, where the unrest first broke out, security officials said.
"The death toll is known to us through various communication intercepts from the militants. They are communicating their losses," said one official who is based in Peshawar.
The official said two paramilitary troops died and seven were wounded when militants ambushed their vehicle in Mir Ali, while one soldier died and two were hurt when a shell hit their security post in Miranshah.
Officials said the military used attack helicopters after bad weather cleared.
"For the past three days we have been receiving reports that a militant leader, Maulavi Abdul Khaleq, wanted to retaliate to avenge the security forces' operations against a militant hideout in Saidgai village on Wednesday," Army spokesman Major General Shaukat Sultan told AFP.
"Today in the afternoon these people started firing rockets at security positions in Miranshah from different directions. The forces responded by using artillery fire," Sultan added.
"The compound of Abdul Khaleq is also engaged and militants also fired rockets from there."
He added later: "It is difficult to say how many militants have died because the operation is continuing through the night. But the army action has been accurate, it has destroyed the targets, particularly their bases from where they were firing rockets."
Local sources said paramilitary artillery fire in Miranshah targeted two hotels, a telephone exchange and a government building which the militants occupied and then fired rockets from.
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