Fresh tensions were sparked between Pakistan and the West after two Nato helicopters operating in Afghanistan allegedly crossed into Pakistan and fired at a checkpoint injuring two soldiers.

Senior military officials have demanded a meeting with Nato commanders after the choppers fired at the post in Pakistan’s North Waziristan, which abuts eastern Afghanistan. The area has been the location of repeated missile strikes by unmanned CIA drones, targeting suspected al-Qa’ida and Taliban fighters.

Reports say the firing took place in the Datta Khel area, west of North Waziristan’s main town, Miranshah. But accounts as to what precisely happened differ. In a statement, Pakistan’s military said: “Two Nato helicopters violated Pakistan air space today…in the early hours of the morning. The troops at the post fired upon the helicopters and, as a result of exchange of fire, two of our soldiers received injuries.”

Nato officials in Afghanistan have confirmed helicopters fired at the border post, but say they only did so after first coming under fire. They have not made clear whether they fired from inside Afghanistan or whether they had crossed the border.

“The International Security Assistance Force (ISAF) is aware of the incident and is assessing it to determine what happened” said a statement. “This effort will be pursued in a cooperative manner using the border coordination centre partnership. ISAF expresses its desire to work with our Pakistani partners.”

While Pakistan’s senior military commanders have tacitly accepted US drones operating in the area, despite growing public condemnation, they have always reacted with deep anger to cross-border incursions by Nato aircraft.

In September 2010, when a previous incursion and shooting incident left two Pakistani troops dead and four wounded, the authorities responded by temporarily shutting down Nato’s supply line that enters into Afghanistan through the Khyber Pass.

The shooting at the border is the latest incident to challenge the often strained relationship between Pakistan and the US. In the aftermath of the operation by US special forces two weeks ago to kill Osama Bin Laden at a compound north of Islamabad, the relationship has become utterly fraught. Many in Washington have said at least some elements within the Pakistani establishment must have been harbouring Bin Laden while Pakistan’s senior military and intelligence have complained, at least in public, about what they consider an affront to the country’s sovereignty.

US Senator John Kerry, who chairs the Senate Foreign Relations Committee, visited Pakistan this week to try and rebuild bridges and at the same time push upon Islamabad the demand of the US that it do more to take on militants. He also secured the return of the wreckage of the US special forces’ helicopter that had to be abandoned during the raid.

Christine Fair, a regional analyst based at Georgetown University in Washington DC, said despite frustration in the US about Pakistan, there was little likelihood of the relationship being terminated. “We don’t have a lot of options but to work with Pakistan,” she said.