Ms Patterson said partisan politics did not determine aid levels to Pakistan
The United States has provided more than $3bn in aid to Pakistan since President Zardari came to power a year ago, its ambassador in Islamabad says.
Anne W Patterson said the money was given in "combined security, economic and development assistance".
She made the comments in response to media reports that US aid to Pakistan was determined on an assessment of the government's performance.
Ms Patterson said partisan politics did not determine assistance to Pakistan.
"The US government will continue to deliver assistance to Pakistan through a variety of long-standing vectors as required by American law to ensure transparency and accountability, and is not depriving the Pakistani government any degree of direct funding as a result of a lack of confidence or trust," the US ambassador said.
Ms Patterson said that some of the anticipated non-military aid would be "directly transferred to the government" and the remainder sent through government institutions and non-governmental organisations.
"There's a huge internal capacity to develop Pakistan, and we want to tap into it," she said.
"Using a deliberate qualifying process, we will stream more funding through national, provincial, and local institutions, and built their capacity to work with us in the future."
Earlier this week, Pakistan's former president, Pervez Musharraf, reportedly said the US military aid given to Pakistan during his tenure had been used to strengthen defences against India.
But in a statement issued on Wednesday, Mr Musharraf, currently on a lecture tour of the US, said Pakistan "never violated any agreement or mis-utilised US funds".
"As far as the equipment issued to a military unit is concerned, the equipment moves wherever the unit is deployed," he said.
The US gave $10bn to Pakistan to fight the Taliban and al-Qaeda.
In 2007, Pakistan rejected a report which said it had used $5bn on weapons systems designed to fight India.
Pakistan's military described the New York Times report as "nonsense".
In May this year, the US announced it was sending $110m (£71m) in aid to Pakistan to help it cope with the refugee crisis in the north-west.