The manual, which is nearing completion, is designed to establish clear rules for targeted-killing operations, the Washington Post reported on Sunday citing unnamed US officials.
However, a major exemption would allow the CIA to continue pounding Al Qaeda and Taliban targets for a year or more before the agency is forced to comply with more stringent rules spelled out in what was described as a counter-terrorism "playbook," it said.
The document, which is expected to be submitted to President Barack Obama for final approval within weeks, marks the culmination of a year-long effort by the White House to codify its counter-terrorism policies and create a guide for lethal operations through Obama's second term, the influential daily said.
Granting the CIA a temporary exemption for its Pakistan operations was described by officials, cited by the Post, as a "compromise that allowed officials to move forward with other parts of the playbook".
"The decision to allow the CIA strikes to continue was driven in part by concern that the window for weakening Al Qaeda and the Taliban in Pakistan is beginning to close, with plans to pull most US troops out of neighbouring Afghanistan over the next two years," it said.
CIA drones are flown out of bases in Afghanistan.
Among the proposed stringent rules are requirements for White House approval of drone strikes and the involvement of multiple agencies - including the State Department - in nominating new names for kill lists, the Post said.
None of those rules apply to the CIA drone campaign in Pakistan, which began under President George W. Bush, it said.