Washington (CNN) -- The Pakistani government has delayed the visas of hundreds of U.S. officials and contractors, a move that has frustrated the State Department and could affect U.S. programs on the ground.

State Department Deputy Spokesman Robert Wood told reporters the reason for the delay was unclear, but it has prompted serious U.S. concerns, and the issue has been raised with "very senior levels" of the Pakistani government.

A senior State Department official who would not speak on the record because of the sensitivity of the diplomacy said Secretary of State Hillary Clinton has spoken with the Pakistani leadership about the visa delays affecting a variety of diplomats and contractors dealing with agriculture, security and military affairs.

"I can't give you any reason why they're being delayed," Wood said. "But we are working with our Pakistani counterparts to try to resolve these issues."

The New York Times on Thursday reported on the delays, quoting American diplomats in Pakistan who called them a deliberate campaign to harass U.S. officials in the country.

Wood said he couldn't point to an "official harassment campaign," but the delays come amid increased anti-American sentiment among the Pakistani public and complaints by the military that the U.S. was meddling in its affairs.

The visas are needed for a planned expansion of the U.S. embassy in Pakistan from about 500 to 800 U.S. officials, to channel a new $7.5 billion, five-year aid plan from the United States.

"I would suspect if this continues, it will indeed have an impact on our ability to do the work that we want to do to help the Pakistani people in terms of fighting terrorism, in terms of economic development, and a whole range of issues," Wood said.

A senior State Department official added that the United States is "not satisfied with the answers we are getting" from Pakistan for the delays. "They are making excuses, saying they are 'working as fast as we can,' but we know for sure that isn't happening."

But Pakistan's ambassador to the United States, Husain Haqqani, denied the delays reflected a campaign of harassment against U.S. diplomats in Pakistan.

"Absolutely not," he said. "We do not harass our allies."

Haqqani said the delays are due to the large influx of U.S. diplomats coming to Islamabad and are "simply a matter of process and conformity of Pakistani rules and procedures."

"There is an exponential number of U.S. diplomats coming in," he said. "In some cases we had 50 diplomats for one issue, now we could have as many as 250. We have to be concerned about their security, our security and also the difficulty of public opinion in Pakistan. But we are partners and allies and we look forward to helping them."