The operation started just after a suicide bomb attack last week on a checkpoint in North Waziristan, a stronghold for al Qaeda-linked Taliban militants on Pakistan's mountainous border with Afghanistan.
Speculation that the army might launch a major offensive in the frontier tribal areas has been building, as the government's attempts to engage the Pakistani Taliban in peace talks have floundered in recent months.
Military officials said more than 30 militants, most of them ethnic Uzbeks, had been killed in the operationl. The army said in a statement: "Security forces exercised utmost restraint to avoid any collateral damage."
The statement didn't address the claims of civilian deaths.
Foreign militants from various countries have long been known to be based in the region.
Pakistani authorities imposed a curfew and residents said many people had fled from their homes after days of shelling and raids by helicopter gunships in the Mir Ali region of North Waziristan following the suicide attack.
Resident Muhammed Tayyab said he lost three of his children and his wife in the shelling. He added: "On the first day of the attack an artillery shell hit the room where my kids and wife were sleeping. The government has put them to sleep forever."
Residents put the civilian death toll at several dozen.
A tribal elder in Mir Ali, who declined to be identified for fear of state reprisals, said: "From the first day of the attack until now 70 civilians have been killed."
Taliban commander Hafiz Gul Bahadur said insurgents would respond by launching a full-scale counter-offensive on army positions if attacks against civilians did not stop.
Residents said bodies were left in the open in the villages of Mosaki and Hasukhel as terrified villagers fled the area.
"We are moving our families to keep them safe but the army's mortars and shells are following us," said Asad Sher of Mir Ali. "Please tell us where is safe."