Reports said many people took to the streets to denounce the operation in which the militants were killed and to demand an investigation.
The people alleged that over 20 men, mostly truck drivers, were shot dead at a restaurant, while shelling claimed several more lives when the army responded to a deadly attack on one of its outposts on Wednesday.
North Waziristan Agency is out of bounds for journalists and independent confirmation of incidents was not possible.
In an apparent response to the allegations, chief military spokesman Maj Gen Asim Bajwa tweeted: "#N. Waziristan: Security forces acted in self defence yesterday and countered terrorists, killing 23 involved in ambush."
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He was also quoted by the media as saying that "only hard-core terrorists were killed". A military rescue team dispatched to the scene of a suicide attack was ambushed by militants in Ippi village late on Wednesday.
Soldiers who pursued the attackers came under fire, including rockets, from a restaurant. Bajwa said troops killed several assailants in a firefight and then entered the building and killed the remainder.
Bajwa said there was "targeted firing on the confirmed locations of the terrorists" and artillery was used only in "extreme" cases.