The General Accounting Office confirmed yesterday that an independent analysis estimates that the 100 B1 bombers the Air Force is buying will end up costing $5 billion to $6 billion more than the $20.53 billion the Pentagon has advertised.

The Air Force, when queried last night, had no rebuttal but is expected to make one today.

In a closed briefing of House and Senate staffers, the GAO released the independent cost estimates for the B1 that the Pentagon had resisted supplying. The Pentagon's Cost Analysis Improvement Group (CAIG), in an independent estimate prepared for Defense Secretary Caspar W. Weinberger, said the 100 B1s in fiscal 1981 dollars would cost either $25.27 billion or $26.7 billion. The higher figure assumes there will be the usual support costs, an assertion the Air Force disputes.

Sen. Carl Levin (D-Mich.), a B1 opponent, said the Air Force has been understating the cost and pressed for release of the higher CAIG estimates.

In another development, Thomas Reed, a former Air Force secretary who yesterday was named a special national security assistant to President Reagan, said the Soviets "are building a B1 type aircraft larger than our B52s."

Although the Pentagon has said previously that the Soviets are building a new bomber, Reed's statement indicates that Washington and Moscow have chosen different paths in building bombers for the 1990s.

The B1 is smaller than the B52, especially in its radar image, to avoid detection. The new Soviet bomber apparently stresses range and carrying capacity.