Kerry, chairman of the Foreign Relations Committee, co-sponsored a bill to provide Pakistan with $7.5 billion over five years. Just $179 million of the first year's $1.5 billion has been spent.
The New York Times reported Monday progress in spending the funds has been slowed because of Washington's fears of Pakistani corruption and incompetence.
Kerry said he is disappointed in the lack of progress in funding projects the aid was intended for but understands why the process is slow.
"I understand that Pakistanis may be frustrated by the slow pace of projects," Kerry said. "Moving this much money transparently through any bureaucracy is always a slow process but the administration must move faster to implement projects."
Other U.S. officials defended the pace at which the funding is being allocated.
"This is a long-term enterprise and building that takes time and we're doing that," said Andrew B. Sisson, the United States Agency for International Development's director for Pakistan.