President Reagan may soon be asked to referee a dispute between the Pentagon and the General Accounting Office over whether the new B1 bomber fleet will cost $20.5 billion, as advertised by the administration, or about $7 billion more.

Pentagon civilian leaders have refused to let the GAO, Congress' watchdog on costs, see two other estimates on how much it will cost to build 100 B1s. Defense Secretary Caspar W. Weinberger, in turning down Comptroller General Charles A. Bowsher on March 22, said releasing such information "would seriously interfere with the decision-making process."

A GAO spokesman said yesterday that the agency is "evaluating the responses" from the Pentagon to see if it should write to Reagan about the impasse and, if that step does not work, go to court.

The GAO and the Drug Enforcement Administration were headed toward a similar showdown recently about records on major narcotics traffickers. But, after the GAO wrote to Reagan, DEA officials agreed to show the agency many of the requested documents, and to provide excerpts of the rest. The GAO and the DEA conferred on the matter yesterday.

On the B1, the GAO is seeking cost estimates provided by two special Pentagon panels. They are Weinberger's Cost Analysis Improvement Group (CAIG), and Air Force Secretary Verne Orr's Independent Cost Assessment panel.

Just as Weinberger refused to show the GAO the CAIG estimates, Air Force Undersecretary Edward C. Aldridge turned down the requests for the B1 price tag given by its independent cost group. To hand over the material, Aldridge wrote the GAO on March 26, "would in the future inhibit the candor" of such discussions between subordinates and superiors.

Under a two-year-old law designed to break such impasses, the GAO can notify the president about the problem, then seek a federal court order for the records 20 days later.

Bowsher's special assistant, Milton J. Socolar, said through a spokesman that the GAO is "evaluating the responses" from Weinberger and Aldridge but has not yet decided whether to write Reagan. Bowsher was traveling and unavailable for comment.

The Pentagon said last year that it could build 100 B1s for $20.5 billion in fiscal 1981 dollars, but the GAO, the Congressional Budget Office and several lawmakers have expressed doubts that this could be done. Because of the cost of building two strategic bombers simultaneously, some critics argue that it makes more sense to drop the B1 and build the more modern Stealth bomber now under development.

Weinberger and his deputies have promised Congress that they will try to keep down the cost of the B1, partly by refusing to let the Air Force make expensive improvements in the plane as the program moves along. The first plane is scheduled to be ready for duty in 1986.

Sources said the CAIG estimate for building 100 B1s was between $27 billion and $28 billion, figures the GAO wants to examine as part of its cost analysis on the program being conducted for Congress.

Although the GAO did not achieve a complete breakthrough with the DEA after writing to Reagan, Tom Colan, the GAO group leader in charge of the drug trafficker study, said yesterday: "We think it's a pretty good agreement."

The DEA agreed to provide GAO auditors full access to many of the requested documents and to supply excerpts of the most sensitive files. The suspects targeted for investigation will be given code names, and the names of confidential informants will be deleted.

Top-level GAO officials will be able to spot check raw data to verify the accuracy and completeness of the summaries provided by the DEA.

Bowsher first complained to Attorney General William French Smith last month before writing Reagan about the drug agency's refusal to let GAO auditors examine the records.