The controversy has erupted just as U.S. President Barack Obama prepares to finalize a plan for stabilizing Afghanistan, Pakistan's next door neighbor, where an insurgency led by the Taliban and supported by al Qaeda has gathered momentum in the past year, causing a growing number of U.S. and NATO military casualties.
Last week, the U.S. Congress approved the Kerry-Lugar bill, named after its sponsors Senators John Kerry and Richard Lugar, which effectively triples U.S. aid to Pakistan to $1.5 billion a year for the next five years. The bill is presently lying with Mr. Obama for signing in to law.
In an attempt to address Washington's concerns over Pakistan's military and its long-suspected ties to hardline Islamic militants, the bill stipulates that U.S. military aid will be withheld if there is evidence that Pakistan is not helping to fight terrorists including al Qaeda and the Taliban.
The bill also seeks Pakistan's cooperation to dismantle illegal nuclear supply networks by sharing "relevant information from or direct access to Pakistani nationals associated with such networks."
This was an apparent reference to Abdul Qadeer Khan, founder of Pakistan's nuclear program, effectively under house arrest for more than five years, since it was revealed that he had traded nuclear know how and technology with Iran, Libya and North Korea. The bill also provides for an assessment of the control of Pakistan's civilian government over the powerful military which has ruled it directly for more than half its life since it became independent in 1947.
Apparently stung by such provisions, General Ashfaq Pervez Kiyani (pictured above), the powerful military chief, on Wednesday met with his top commanders at the Pakistan army's general headquarters in Rawalpindi - a suburb of Islamabad, the Pakistani capital.
"The forum expressed serious concern regarding clauses impacting on national security," said the military in a statement after the meeting, acknowledging that part of the discussion was on the Kerry-Lugar bill.
The military further said it was providing the government of President Asif Ali Zardari and Prime Minister Yusuf Raza Gilani who both support the Kerry-Lugar bill with its "formal input" over the issue. The statement also said it was the parliament that would debate the issue and finally enable the government to respond.
Western defense experts familiar with Pakistan's military said the army's reaction to take a public stand suggested that the generals were seeking to at least share their reservations on a U.S. bill which has so far has been debated and publicly discussed by the country's ruling politicians.
General Kiyani is widely known to be a liberal figure who has had extensive dealings with senior U.S. and NATO generals. However, his decision to take a position on the Kerry-Lugar bill indicates a wider resentment among top generals according to western defense analysts.
"The military feels they have to publicly take a position on this matter," said one western defense official in Islamabad who spoke to CBS News on condition of anonymity. "The Pakistani military is not at all anywhere near seeking to break ranks with the U.S. What they seem to be doing is simply taking a stand. Now, the next step will come from Washington where President Obama may not want to see a break in relations with Pakistan, especially as he (president Obama) deals with the crisis in Afghanistan."