While the drone strike successfully targeted Taliban fighters, the official argued "that's not the point." It increased anti-American sentiment and therefore makes it more difficult for the military to work with the U.S., he said.
"You are putting the government and military in such a tight position, there will be no other choice than to respond," he said, adding that the U.S. would have to "face the consequences" of whipping up media criticism against the Pakistani government and military.
Asked how the military might respond, he said only, "There are always leverages, even for the weaker side."
U.S. officials declined to comment on the Pakistani military official's accusations. But the U.S. embassy in Islamabad released a statement insisting that throughout Mullen's visit, he "emphasized the long-term U.S. commitment to supporting Pakistan in its fight against violent extremists."
Pakistani military and government officials say the ISI wants to return to the days when the drone program started, when the CIA provided more advance warnings of drone targets. Back in 2006, the military official said, the relationship was so much better than it is now that the Pakistan Army pretended it had accidentally bombed a school in order to cover up an errant CIA strike.
"That's the kind of relationship we had back then," the official said. "Could you imagine us doing that now? No way." Today, though it even still helps provide some intelligence for strikes that kill Pakistani militants, the Pakistan Army has criticized two drone strikes in a row.
But what the Pakistani military is also after, the senior official admitted, is a list of all U.S. intelligence officials in Pakistan and their agendas.
Early after 9/11, he and other Pakistani officials say, CIA officials were allowed to enter Pakistan in bulk, and the government was "clueless of the number, the assignments," the senior official said.
The military used the detention of Ray Davis – the CIA contractor who shot and killed two men in January who some officials say were working for the ISI – as an excuse to clamp down on the American operatives.
"The system had become loose," the senior Pakistani military official said. "We felt we lost control."
The frustration extends to Afghanistan, where the U.S. and Pakistan are positioning themselves for an endgame that will involve political negotiations with insurgents.
The senior Pakistani military official accused the U.S. of purposely withholding its long-term strategy for Afghanistan.
"That leaves you guessing what your so-called coalition partner is up to," he said. "And without a U.S. plan, how does Pakistan create a plan? We're groping in the dark."
There are also other conflicts between the two governments. The U.S. is concerned that Lashkar-e-Taiba, the Punjabi militant group that attacked Mumbai in 2008, is being shielded by the ISI. The senior Pakistan official said he "understood the concern," but painted it as totally inspired by Indian officials.
"Somewhere in the middle of this relationship, the Indians prevailed," the official insisted.
And there is lingering sourness over the Davis detention, which in the words of the Pakistani military official, "couldn't have been handled worse" by U.S. diplomats.
But U.S. and Pakistani officials -- including the senior military official -- were quick to insist that the relationship will survive, if only because it is too important.
"Help us help you," said the official. "If you're not interested in that, how do you expect us to help you?"