In a dispatch from Islamabad, The New York Times said some Pakistani officials are convinced that the Americans deliberately fired on their military, killing 11 men from the Frontier Corps the Americans want to train.
But, according to The Times, the Americans deny that conclusion. The $400 million training programme is intended to combat militancy by fielding the FC, from among the tribes that live in the border areas.
Ending or delaying the programme, which is already under way, would deny the United States what little leverage it has in the tribal areas to combat a rising number of cross-border attacks into Afghanistan against American and Nato forces this year, the paper said.
The United States military claimed the air strikes had been carried out in self-defence against militants who had attacked American forces in Afghanistan and then fled into Pakistan. But the Pakistanis continue to dispute the American account.
"This is the first time the United States has deliberately targeted co-operating Pakistani forces," Jehangir Karamat, a former chief of the Pakistani Army and a former ambassador to the United States, was quoted as saying. There has been no statement by the United States that the intention was not to target Pakistani forces, he said.
"The recriminations have exposed the underlying mistrust in the alliance, which has been held together in large part by the personal relationship between President Pervez Musharraf and President Bush," the Times said, citing Pakistani officials and diplomats.
As the two men "fade" from power, the alliance is finding it difficult to quell the threat to the United States, Afghanistan and Pakistan from a growing array of Taliban and al Qaeda cells, Times correspondent Jane Perlez wrote.
A senior Pakistani government official with long experience in military affairs, one of the two Pakistani officials who spoke on the condition of anonymity because of diplomatic sensitivities, summed up the feeling of many in the Pakistani military, saying the strikes appeared deliberate despite American denials and intended to "punish" Pakistan for not preventing the militants from crossing into Afghanistan.
In Washington, the Pentagon press secretary, Geoff Morrell, expressed regret for the death of the Pakistani soldiers, but did not acknowledge any American culpability pending an investigation by senior Pakistani, Afghan and American officers.
The American, Afghan and Pakistani militaries have agreed to hold a joint investigation into the strikes. That inquiry will now have to sort out the conflicting accounts in an extremely charged atmosphere.
Pakistan vehemently denies the American claim that the raid was in self-defence, saying the bombs were aimed at a Frontier Corps post at Gora Parai, about 100 miles north-west of the town of Ghalanai.
A stone hut and seven of nine bunkers in which the soldiers were seeking cover were destroyed, the Times said, citing Pakistani officials. The co-ordinates of the post were clearly marked and were known to Nato and American forces, they say. The senior Pakistani government official with military experience said the strikes were "too accurate and too intense" to have been an accident.
Whatever the case, the fury over the air strikes was such that Army Chief General Ashfaq Parvez Kayani "personally approved an unusually strong statement last week from the Pakistani military, which called the strikes cowardly and unprovoked," the dispatch said, citing Pakistani officials.
According to the dispatch, American officials have said that General Kayani has refused every suggestion of letting American forces operate in the tribal areas, even on an advisory basis. A plan for American trainers to accompany Pakistani troops on missions to root out insurgents in the tribal areas was ruled out completely, a senior Pakistani military official said.
The plan for American military advisers to instruct Pakistani trainers, who would in turn train Frontier Corps units in counterinsurgency tactics, was accepted by General Kayani as a light-footed alternative, American officials have said.
"Even so, there is considerable scepticism in Washington and among United States military commanders about the value of the training, and the strains caused by the air strikes have now brought into the open blunt expressions of dissatisfaction with the Pakistanis that officials had kept mostly private," the dispatch said.
A major reason for the distrust of the Americans among the Pakistani military came from the belief that Pakistan was unfairly blamed by Washington for the American and Nato difficulties in the war in Afghanistan, it said.
The struggle against the Taliban in Afghanistan was faltering not only because Taliban were crossing the border into Afghanistan, the Pakistani government official said. "Pakistan thinks you have screwed up in Afghanistan and made Pakistan the fall guy," the official said.