WASHINGTON (AP) _ The chairman of the House Intelligence Committee says he cannot accept President Reagan's agreement with two Senate Intelligence panel leaders on a new policy for disclosing covert operations.

The agreement with Sens. David Boren, D-Okla., and William Cohen, R-Maine, the chairman and co-chairman of the Senate Intelligence Committee, provides that the president notify the congressional intelligence committees within ''two working days,'' but says this new disclosure policy should exclude ''the most exceptional circumstances.'' The agreement was announced Friday.

But Rep. Louis Stokes, D-Ohio, chairman of the House intelligence panel, said he does not believe the president has the power to ''fully establish key principles of congressional oversight of intelligence.'' Instead, he said, the laws have to be changed.

''I cannot accept the president's assertion that he possesses inherent constitutional authority to bypass statutory requirements for prior notice of covert actions,'' Stokes said in a statement issued Friday.

''When the president withholds information from the intelligence committees so as to prevent consultation, he thwarts the exercise by Congress of its constitutional responsibilities,'' he added.

Stokes has introduced legislation requiring that the president notify Congress within 48 hours of the inception of an intelligence operation.