The findings said interference by Pakistani officials reached “new levels of intensity” in 2011.
The US raid on Osama Bin Laden’s compound and a Nato air strike that killed 24 Pakistani soldiers were identified as turning points.
Recent months have seen a marked deterioration of US-Pakistan relations.
Pakistan withdrew military co-operation in the wake of the deadly November air strike, and correspondents say it marked a change in relations between the two countries.
The report, by the state department’s inspector general, acknowledged that the Pakistani government had previously interfered with US officials on its soil.
The report is strikingly blunt. Events of 2011 have had such an impact on relations between Washington and Islamabad that US diplomats in Pakistan are struggling to do their jobs. Meddling officials have long been a frustration, but in asking for the concerns to be raised in continuing dialogue, the state department is hoping that Pakistan will cut them some slack.
The US feels Pakistan should be more pro-active in combating militants, but it must balance its frustration with the need to keep a military ally. This report is yet another sign that in Washington, patience with Pakistan is wearing thin.
However, it said the problem had become much worse and recommended that the issue should be taken up by the US with Pakistan at the highest levels of government.
“Official Pakistani obstructionism and harassment, an endemic problem in Pakistan, has increased to the point where it is significantly impairing mission operations and program implementation,” the state department review said.
It described the harassment as “deliberate, wilful and systematic” and said examples of the obstruction included delays in getting visas, holding up shipments for construction projects and aid programmes, and surveillance of employees.
The report also claimed US officials were being singled out more than other international diplomats.