Farhatullah Babar, President Ali Asif Zardari's chief spokesman, said previous U.S. aid packages negotiated under Gen. Pervez Musharraf, who ran a military government here for eight years beginning in 1999, contained similar clauses and the army never complained.
"Why this protest now?" he asked.
He also said the army should not have gone public with its concerns.
"There are proper forums like the defense committee of the Cabinet and the Ministry of Defense for communication of such views and participating in the decision making process," he said. "Why this was bypassed, I don't know."
He strongly defended the aid package, saying "there is nothing against the national interest in the bill."
Among other strings, the bill conditions U.S. aid on whether Pakistan's government maintains effective control over the military, including its budgets, the chain of command and top promotions. The U.S. bill also includes yearly certifications that Pakistan is making a sustained commitment to combating terrorist groups and cooperating in stopping the proliferation of nuclear weapons.
Some analysts said the military's statement had little to do with genuine dislike of a bill that stands to help crumbling schools, roads and hospitals. They said the army was sending a message to the Pakistani and U.S. governments about the limits of civilian control in a country that's been subject to military rule for about half of its 62-year history.
In a sign the aid also was causing rifts within Zardari's civilian government, coalition partners expressed reservations over the aid, and said their support for it could not be guaranteed.
"Two groups of our lawmakers and legal experts are deliberating on this issue," said Haider Rizvi, a lawmaker from the Muttahida Quami Movement.
Senator Zahid Khan of the Awami National Party, which is also in the government, said the party was expected to make a decision on the aid next week.
U.S. diplomats reached out to Pakistani officials Thursday to ease concerns about the bill, which awaits President Barack Obama's signature, said spokesman Richard Snelsire. He declined to give more specifics.
The army's resistance complicates America's anti-terror strategy in South Asia, much of which rests on alleviating poverty in the nation of 175 million to lessen the allure of extremism.
As the debate raged on, helicopter gunships and artillery batteries shelled militant positions in several areas of South Waziristan, in what could be a prelude to a planned offensive against militants there, intelligence officials and witnesses said. Residents said several compounds were hit and people were fleeing for safety.
The military has not given a timeframe or a description of the offensive, and it was not clear if it would be a limited one relying mostly on air power or a fully fledged operation with thousands of ground troops aimed at clearing and holding the whole region.
The U.S. sees a Pakistani offensive against the militants in the lawless tribal regions as crucial to its own war against the resurgent Taliban and al-Qaida in neighboring Afghanistan, and it was heartened by the army's recent offensive against the Taliban in the Swat Valley.
But the army has been beaten back in South Waziristan three times since 2004 and analysts say 10,000 well-armed militants, including foreign fighters, are dug in around the harsh terrain of the region.
In other violence, the army said it killed 17 militants in fighting in Swat.
Associated Press writers Zarar Khan, Nahal Toosi and Munir Ahmad in Islamabad, and Ishtiaq Mahsud in Dera Ismail Khan contributed to this report.