Protesters packed the streets in Pakistan throughout the weekend, condemning Saturday's cross-border attack.
On Monday, Pakistan's military claimed the airstrikes continued for two hours despite pleas with coalition forces to stop. An army spokesman alleges they were ignored when they contacted NATO counterparts while the attack was going on.
Pakistan also denies claims from Afghan officials that NATO and Afghan forces took incoming fire from the direction of two Pakistani checkpoints before the airstrikes.
In the past NATO officials have claimed that insurgents have fired across the mountainous border into Afghanistan, from locations close to Pakistani soldiers that have been accused of sympathizing with militants.
The attack has fueled previous-held Pakistani sentiments that the US and NATO are hostile to Pakistan.
"Whoever is a friend of America is a traitor to the land," members of an alleged front group for the militant Lashkar-e-Taiba organization, chanted in a demonstration in Karachi.
NATO promised a full investigation and described the incident as "tragic and unintended."
On Monday, President Barack Obama extended his sympathy to the dead soldiers. Spokesman Jay Carney said that the administration is looking into the circumstances of the incident.
The U.S. had been hoping to enlist Islamabad's support to end the 10-year-old war in Afghanistan. The recent attack has deepened tensions and has been a major setback in the fight against Taliban and Al Qaeda forces.
The Associated Press contributed to this story.