The bill, co-authored by senators John Kerry and Richard Lugar, also provides for an assessment of how effective the civilian government's control over the powerful military has been.
Shah Mehmood Qureshi, the Pakistani foreign minister, raised concerns over the language in the bill, conveyed to Kerry the sovereignty worries raised in parliament and said they needed to be addressed.
|Pakistan is concerned over some of the conditions tied to US non-military aid [EPA]
Qureshi also said Pakistan "will not compromise on its sovereignty" and "will not allow micro-management" of military operations in his country.
Kerry promised a written clarification within 24 hours to explain some of the terms that he described as having been characterised inaccurately "in some quarters".
"The bill doesn't have to be changed," he said after meeting Qureshi in Washington.
"If there is a misinterpretation, it simply has to be clarified."
Kerry reiterated that the bill did not impinge on Pakistani sovereignty, and that he was confident "we will not only be able to adequately address the concerns that have been raised in Pakistan but we will provide a clarity that has force of law".
Wendy Chamberlin, a former US ambassador to Pakistan, told Al Jazeera the US approved a large aid programme to the people of Pakistan with the aim of closing the "trust gap" that has existed for decades.
She said the package was well received by Pakistanis, but the tune later changed after the civilian government came under pressure from the army which took issue with some of the language in the bill.
"The bill was not meant for the military, it was meant for civilians, but it did have some unfortunate language in there that they took umbrage with.
"The real tragedy here is that the intention of the bill is to help build trust between the US and Pakistan, but ended up having the opposite effect," she said, adding that US diplomats needed to address the concerns.
Qureshi also met Richard Holbrooke, the US special representative to Afghanistan and Pakistan, and James Jones, the US national security adviser.
The US is the biggest aid donor to Pakistan and counts on Islamabad's help in its hunt for al-Qaeda leaders and in stopping fighters from crossing the border into Afghanistan to fight US-led forces there.