Pakistan has asked the US to reduce the number of CIA agents in the country and to limit drone strikes along the Afghan border, US media reports say.
The reports quote unnamed officials and come as US and Pakistani spy chiefs met at the CIA's US headquarters.
An official spokesman described those meetings as "productive".
Relations between the two countries have been frayed since a CIA contractor shot dead two men in the city of Lahore earlier this year.
Last month a Pakistani court freed Raymond Davis after acquitting him of two counts of murder, when relatives of the two men he shot dead pardoned him in court.
Mr Davis maintained the men had been trying to rob him.
The case stoked anti-American feeling across Pakistan and led to angry demonstrations - particularly when it emerged that he worked for the CIA. Hardline religious parties were keen to see him punished.
The continuing diplomatic strains emerged as CIA Director Leon Panetta met the head of Pakistan's Inter-Services Intelligence directorate, Ahmed Shuja Pasha, in the US state of Virginia.
The New York Times reported that about 335 US personnel, CIA officers and contractors and special operations force personnel were being asked to leave Pakistan. It quoted an unnamed Pakistani official said to be closely involved in the discussions.
Pakistan also wants the removal of CIA contractors on assignments that Pakistan have not been informed about, Pakistani officials told the paper.
The officials estimated that would account for 25%-40% of CIA staff in the country. The reduction in CIA operations appears to have been personally requested by Pakistan's army chief Gen Ashfaq Kayani.
Pakistan is also demanding restrictions in the US drone campaign aimed at eliminating militants in Pakistan's restive north-west, another unnamed Pakistani official told the New York Times.
But unnamed US officials quoted in the New York Times report denied any request had been made to reduce the number of CIA agents in Pakistan.
CIA spokesman Preston Golson told Reuters news agency: "Director Panetta and General Pasha held productive discussions today and the CIA-ISI relationship remains on solid footing."
US drone attacks have escalated in north-west Pakistan since President Barack Obama took office. More than 100 raids were reported in the area last year.
The US does not routinely confirm it is conducting drone operations in Pakistan, but analysts say only American forces have the capacity to deploy such aircraft in the region.
Drone attacks are hugely unpopular with the Pakistani public. Correspondents say they have the tacit approval of the authorities, although Pakistani leaders deny secretly supporting the strikes.
Many militants, some of them senior, have been killed in the raids, but hundreds of civilians have also died.
Several incidents over the last year have underscored the difficult relations between the US and Pakistan:
* One day after Raymond Davis was released in March, a drone strike killed many civilians, prompting an unprecedented outburst against the attacks from Pakistan's army chief
* In late 2010 Pakistan temporarily shut a key border crossing because of a Nato air strike which killed two Pakistani soldiers
* The previous undercover CIA chief in Pakistan was forced to leave the country for safety reasons once his name was published in a Pakistani lawsuit
Tuesday's reports follow a candid interview that Pakistan's President, Asif Ali Zardari, gave to Britain's Guardian newspaper on Monday saying that the Afghan war was "destabilising Pakistan".
He also rejected a recent White House report which said Pakistan lacked its own plan to fight insurgents in the country, adding that most US politicians lacked an understanding of the situation.
The BBC's Syed Shoaib Hasan in Karachi says Mr Zardari's interview comes at a time when many in Pakistan feel that the US is blaming the country's instability while directly contributing to it with its actions along the Afghan border.
Mr Zardari's statements are likely to meet with approval from Pakistan's security establishment, which increasingly feels the US is taking its Pakistani alliance for granted, our correspondent adds.