The criticism made in a statement after the monthly meeting of the nation's top generals embarrassed the government of President Asif Ali Zardari and came as the Obama administration is seeking to persuade the Pakistani army to broaden its campaign against the Taliban and Al-Qaida in Pakistan.
The chief of the Pakistani army, Gen. Ashfaq Parvez Kayani, was so offended by stipulations in the American legislation that he complained to the American commander in Afghanistan, Gen. Stanley A. McChrystal, when the two men met in Islamabad on Tuesday, according to a senior Pakistani military officer.
The legislation passed by Congress last week gives Pakistan $1.5 billion over the next year for the Zardari government to build roads, schools and other infrastructure, a gesture intended to shore up the weak civilian government and turn around the widespread antipathy toward the United States among Pakistanis.
Instead, the aid package has served to widen the distrust between the powerful military and the civilian government, even though the new aid comes in addition to America's aid to the Pakistani military, which had totaled more than $10 billion since 2001.
The section of the legislation that has outraged the army says the secretary of state must report to Congress every six months on whether the government is exercising "effective civilian control over the military."
The secretary must assess the extent to which the civilian government has oversight over the military chain of command, promotion of generals and the military budgets, provisions that even Pakistani politicians have taken strong exception to as meddling in Pakistan's own business.
The legislation also says Pakistan has to show progress in ceasing its support for terrorist groups, and dismantle groups operating out of two places, Quetta and Muridke.
The generals were specifically infuriated by mention of Quetta, which the Obama administration says is a base for Taliban who fight American forces in Afghanistan, and of Muridke, which is a well known base for Lashkar-e-Toiba, a militant group formed two decades ago by the Pakistani government to fight India.
The United States and India say Lashkar was behind the attacks in India's financial capital, Mumbai, last November that killed 163 people.
"This is a direct indictment," a senior military official said in reference to Muridke. The Americans, he said, were threatening the Pakistanis, saying that if the Pakistani military did not behave according to American wishes, then the Americans would penalize them. "Some may say this is typical American arrogance," the official who spoke candidly on condition of anonymity said.
Anger over what is being interpreted as impudent American demands has been building, fanned by other recent frictions - plans for a bigger American embassy, the use of an American private security firm to protect American diplomats - in what was supposed to be a new era of better relations between the United States and Pakistan under President Barack Obama.
The fury reached a high on Wednesday, even exceeding longtime complaints about American drone attacks against militants in the tribal areas as being an infringement of sovereignty.
In its statement after the generals' monthly meeting, the army said: "The forum expressed serious concern regarding clauses impacting on national security." A "formal input" by the military would be sent to parliament, the army said.
Zardari held a lengthy meeting with members of his Pakistan Peoples Party on Tuesday, many of whom were having difficulty explaining the aid legislation under a barrage of criticism in the press and among the opposition parties.
Afterward, the presidential spokesman called the attacks on the legislation "propaganda" aimed at "undermining" the president's position.
Part of the military's anger focused, the senior military official said, on the affront of not being informed by the civilian government over the stipulations that affected the army.
"The security establishment of the country has not been kept in the loop," he said.
The front-page headline on Wednesday for a story about the meeting between Kayani and McChrystal in the influential newspaper The News read: "Insult! Army tells USs military."
In a conciliatory address to parliament on Wednesday evening, the prime minister, Yousaf Raza Gilani, argued the legislation was not binding. He assured parliament that the government would "never" allow a foreign power to have access to the nation's nuclear assets.
The prime minister's reference to Pakistan's nuclear capability was apparently to allay anger about a reference in the legislation asking Pakistan to continue to cooperate with the United States in efforts to dismantle networks trying to acquire nuclear weapons related materials.