"The insurgents were monitored, tracked and subsequently engaged in Afghanistan, through the coordinated use of both air and ground fire in a series of engagements along the sparsely populated border region," it said.
Nato said initial battle damage estimates indicated as many as 150 people were killed. It did not say if there were any casualties among Nato or Afghan government troops.
Nato said Pakistani military liaison officers were kept fully informed throughout the operation.
Afghan anger over the infiltration of Taliban fighters from Pakistan has seriously soured relations between the neighbours, both important US allies in the war on terrorism.
Last year was the bloodiest since US-led forces overthrew the Taliban in 2001.
More than 4,000 people, including nearly 170 foreign troops, were killed.