CIA Director Leon Panetta and the ISI chief Lt Gen Ahmed Shuja Pasha had a four-hour long meeting on Monday at the agency's headquarters at Langley, which is across the river from the White House.
“Director Panetta and General Pasha held productive discussions yesterday, and the CIA-ISI relationship remains on solid footing,” CIA spokesman George Little told Dawn .
“The United States and Pakistan share a wide range of mutual interests, and yesterday's exchange emphasised the need to continue to work closely together,” he said.
Both sides agreed also to work closely “on our common fight against terrorist networks that threaten both countries”.
Senior US military officials also attended the meeting with the ISI chief and other Pakistani military officials. Pakistan's ambassador in Washington, Husain Haqqani, however, did not participate in the talks.
After the meeting, the ISI chief left abruptly for Islamabad, causing wild speculations in the US capital as both US and Pakistani media had reported that he was here on a three-day visit.
But Pakistani and US officials rejected these speculations as incorrect, claiming that it was only a one-day visit and Gen Pasha's departure on Monday evening was part of the official schedule.
Diplomatic sources told Dawn that Pakistan conveyed to the CIA chief its “reservations on the size, scope and activities” of the US agency's team in Pakistan.
Mr Panetta is believed to have asked for more details.
Pakistan also told the CIA boss that the agency's drone strikes inside Fata had become counter-productive and urged him to discontinue the attacks.
“If an occasional strike is required in an inaccessible area, it should be conducted with Pakistan's coordination,” said an official familiar with the talks.
“But the most important point that the Pakistanis stressed was that they no longer trust a verbal understanding on CIA activities inside their country,” the official said.
“They have asked for a more formalised arrangement. They want everything on papers.”
The CIA is believed to have asked for more time to work out the details.
Despite the controversial nature of the issues raised in the Panetta-Shuja meeting, both sides stressed that the CIA as well as the ISI wanted their relationship to continue.
They also agreed that the CIA should issue an official statement about the proceedings of the meeting, stressing the need for continued cooperation between the two allies.
Meanwhile, the US media noted that Monday's meeting followed a string of recent events that highlighted the increasing disagreements between the two sides on how to move forward against extremists in Pakistan and neighbouring Afghanistan.
Media reports said that Islamabad was seeking the withdrawal of over 300 US operatives from the country. This represents anywhere from 25 per cent to 40 per cent of US special operations forces in Pakistan.
Media reports also noted that the arrest and subsequent release by the Pakistani authorities of CIA security contractor Raymond Davis exposed the extent of the CIA's network in the country. Mr Davis shot dead two Pakistanis in Lahore in January but was freed after more than $2 million in “blood money” was paid last month to the relatives of those killed.
The incident showcased the discord between the allies and gave voice to previously muted concerns in Islamabad that US counter-terrorism efforts were undermining Pakistani sovereignty, the US media observed.
Another sign of growing tensions between the two countries came last week, when the White House warned that Pakistan still had no concrete plan to eliminate violent extremist groups on its territory.
Washington insiders say such public criticism is only a small part of the long list of complaints that senior US officials have held for years.
Meanwhile, an American official told the Washington Post on Tuesday that Mr Panetta and Mr Pasha had a conversation that reflected a sense of partnership and desire to move forward. “This wasn't some kind of ultimatum session, as some press reports have suggested it might be. The two leaders discussed common interests and a few concerns, all of which can be sorted out.”
The Post's associate editor and columnist David Ignatius reported that he was unable to verify media reports that Pakistan had asked the US to withdraw 335 CIA officers, agency contractors and Special Forces operatives.
“That number wasn't possible to verify in Washington. That number apparently didn't come up in the Panetta-Pasha meeting, and an ISI source in Pakistan said on Tuesday that he couldn't confirm it, either,” Mr Ignatius reported.