The Pentagon yesterday disputed Congressional Budget Office claims that the B1 bomber would cost almost $40 billion and tried to limit some self-inflicted damage to the program by issuing an unusual letter "intended to clarify" some earlier remarks made by Defense Secretary Caspar W. Weinberger.

During a round of appearances on Capitol Hill, the Pentagon's top scientist, Richard D. DeLauer, and the Air Force chief for research and development, Lt. Gen Kelly H. Burke, both insisted that the program to build 100 B1 bombers would be held to the official $20.5 billion estimate as measured in current prices, or $28 billion when inflation is included.

After a closed-door briefing of the Senate Appropriations subcommittee on defense, Burke told reporters, "We have high confidence we'll deliver at that cost." He said that the CBO used a different inflation estimate than the administration's and "included a large number of items that we have no intention of putting on the B1."

DeLauer said that some other B1-related costs were budgeted in other parts of the Air Force budget.

The Senate panel has wrapped up work on the $208 billion defense spending bill but decided yesterday not to vote specifically on the $4.1 billion requested for the two most controversial programs--the B1 bomber and the MX missile--in President Reagan's newly announced plan to "rearm America."

Rather, the panel's chairman, Sen. Ted Stevens (R-Alaska), said the full Appropriations Committee will hold final hearings Monday and vote on Tuesday.

The Pentagon's efforts in Congress yesterday, however, appeared to ease at least some of the suspicions about the bomber project. Stevens, who has been critical in the past, said he was now convinced that, even at the higher price, the B1 is worth it.

He said the bomber should be built as quickly as possible to avoid even higher costs and to hasten the day when the older B52 bombers can be taken out of service, which also saves money.

Stevens said the panel would recommend 3 percent more than the administration asked for in the B1 and MX projects because that is a more realistic estimate of the cost and would prevent even costlier future delays.

Sen. Warren Rudman (R-N.H.) said he felt a key factor in favor of the B1 would be a Pentagon analysis that DeLauer later presented to a Senate Armed Services subcommittee. This showed it would cost $93 billion between now and the end of the century to modify and keep the current fleet of more than 300 older B52 and FB111 bombers flying, compared with about $114 billion for a new fleet of 100 B1s and 132 of the more futuristic Stealth radar-evading bombers.

Sen. Jake Garn (R-Utah) said it would be "tragic" to play politics with the B1 and stop it and that even "the wildest" cost estimates being used are only equal to "about 2 1/2 years of food stamps."

Garn said he would "bet anyone" that the Stealth bomber would not be operational before 1995 at the earliest, which means that the B1 is needed to fill that 10-year gap from 1986, when the first bombers become available to the mid-1990s.

In recent weeks, Weinberger has told Congress that the Stealth could be operational by 1989 and that the B1 might not be able to penetrate Soviet air defenses after 1990. These were both damaging to the Air Force case because it suggested only a short period when the extremely expensive B1 would be needed.

Yesterday, a joint letter was sent to Stevens by Weinberger and CIA chief William J. Casey, saying that the new B1 "would have the capability to penetrate anticipated Soviet air defenses well into the 1990s."

DeLauer also indicated that the Stealth was not likely to be operational by 1989. Sen. Carl Levin (D-Mich.) was sharply critical of the apparently wrong assessments given by Weinberger and the explanations offered for them by DeLauer.

"I think if we meet often enough, we are going to do wonders" with these programs, Levin quipped in reference to the frequent shift in assessments.

Levin demanded that DeLauer supply a copy of a reported internal Pentagon cost study that put the B1 price at $28 billion without inflation. DeLauer, who acknowledged that he attended a study group meeting, said he could not remember what the estimate was.