An unnamed military official was quoted by the Dawn newspaper as saying the onus was on the CIA to take the relationship back to the level it was at prior to Davis' arrest last month.
Both the official and chief military spokesman Maj Gen Athar Abbas refused to comment on or deny reports of a direct contact between CIA chief Leon Panetta and ISI head Lt Gen Ahmed Shuja Pasha.
Media reports had said Panetta had spoken to Pasha on phone regarding the controversial issue of Davis. The ISI had also sought a list of all CIA operatives in Pakistan, the reports said.
Relations between the ISI and CIA have been in the eye of the storm since Western media reports revealed that Davis was a security contractor working for the CIA.
Reports also said Pasha had sought details of all CIA operatives in Pakistan during his conversation with Panetta on Wednesday.
The unnamed military official said the arrest of another American national from Peshawar, who too is suspected of being a CIA operative, indicated that many more CIA men might be operating inside the country without the knowledge of Pakistan.
"We are doing a lot for them and we must not be treated the way we are being treated," the official said, pointing out that there were 80,000 US troops in Afghanistan that are dependent on Pakistan.
Several political analysts have noted that the Pakistani military may be using the row as an opportunity to check US officials and CIA operatives within Pakistan.
The Pakistani military is also not happy with the liberal visa policy the current government has implemented for Americans.
The analysts have conjectured that a "quid pro quo for the release of Davis, if and when it happens, may be more military supervision of American nationals entering the country", the report said.
Though former Pakistan Army chief Gen Aslam Beg had claimed that Davis was heading a team of 3,000 CIA officials and operatives in Pakistan, a military official told the Dawn that they were estimated to be in hundreds and not thousands.