Defence Minister Ahmed Mukhtar said members of Inter-Services Intelligence were accused of “tipping off” militants before strikes in the tribal areas.
Mr Mukhtar said that the Americans “mistrusted” the ISI.
His unusual public admission of the rebuke seems to mark a new low in ties between the US and Pakistan’s spies.
‘Who’s in charge?’
Mr Mukhtar was speaking in Washington, where he is accompanying Prime Minister Yousuf Raza Gilani on his first visit to the US.
Speaking on Pakistan’s Geo TV, he said the Americans had alleged that information about targets was being “leaked”.
“The burning issue of course is as to who controls the ISI,” he said.
“In their [the Americans’] view there are some people at some level in the ISI who tip off the Taleban at some level about impending missile attacks when these are shared with the Pakistanis.
“They [the Americans] have expressed displeasure over this.”
Mr Mukhtar also openly admitted that President Bush had asked who was really in charge of the ISI during the visit to Washington.
The BBC’s security correspondent Rob Watson says that relations between the American Central Intelligence Agency (CIA) and the ISI appear decidedly strained.
Our correspondent says that the stern message apparently being delivered to Islamabad was that Pakistan has to do more to tackle ties between the ISI and Islamic extremists based in the country’s tribal areas.
By the way, Infowars' most powerful product is back in stock! Get DNA Force Plus up to 50% off now!