According to The New York Times, US officials say the treatment includes refusing to extend or approve visas and frequent car searches.
"They don't want more Americans here. They're not sure what the Americans are doing. It's pretty pervasive," one American diplomat was quoted as saying.
But the harassment is now affecting operations in the country, the report said.
American helicopters used by the Pakistani military can no longer be used because visas for 14 American mechanics have not been approved.
"There's an incredible disconnect between what they want of us and the fact we can"t get the visas," another diplomat said.
But Pakistani officials say the treatment is a response to American arrogance and provocation, not harassment.