The two helicopters intruded into the Kurram Agency from Afghanistan's Paktia province before dawn and when security personnel deployed at the Mandato Kandaou post, 15 kilometres west of Parachinar, fired warning shots the helicopters fired missiles.
Sources said that the Nato helicopters had intruded up to 5km across the border.
The incident heightened tension in the region and the government immediately suspended supplies to foreign troops in Afghanistan via Torkham.
An official of the Khyber Agency administration told Dawn that the Frontier Corps had stopped loaded trucks and oil tankers from entering Afghanistan.
According to ISPR, two helicopters from Afghanistan appeared to have crossed the border into Pakistan at Mandato Kandaou in the Ali Mangola area of Upper Kurram Agency and engaged through cannon fire an outpost of the Frontier Corps located 200 metres inside Pakistan and manned by six soldiers.
Troops at the post retaliated with rifle fire to indicate that the helicopters were crossing into Pakistan's territory. Instead of heeding the warning, the helicopters fired two missiles, destroying the post.
The ISPR statement said this was the third incident of its kind in a week.
Hours later, two Nato helicopters entered Kurram Agency again and fired at least seven rockets which landed near the Akhtar Ghundai post in Matta Sangar area, southwest of Parachinar.
No casualty was reported. Soon after the attack, local authorities closed the Borki point for cross-border movement.
After a similar incident on Sept 27, contact was made at the highest military level and the incident was regretted by the US.
The third violation of Pakistan's airspace by Nato in a week is seen by many as part of a plan to extend the Afghan war into Pakistan.
Meanwhile, the US embassy denied reports about a veiled threat by Nato Commander Gen David Petreaus to launch ground operations inside Fata if the government refused to dismantle a militant network in North Waziristan. “This allegation is false. Gen Petreaus made no threat of ground operations inside Pakistan,” it said.
Khyber Pakhtunkhwa Governor Owais Ghani said that it was not the first incident of its kind and Nato must explain how its modern army could possibly mistakenly attack Pakistani soldiers at the very well-known border post.