The Congressional Budget Office estimated yesterday that it would cost $39.8 billion, well beyond what the Pentagon has claimed, to build and equip the 100 B1 bombers President Reagan is seeking as part of his plan to rearm America.

CBO's new estimate, which includes some equipment that the Pentagon does not count, works out to almost $400 million for each bomber, or more than 40 percent above the Pentagon's advertised price of $280 million. It would make the B1 easily the most expensive warplane ever built, and is certain to plunge the new bomber into deeper controversy.

"There is deep division over the need and the cost of this strategic bomber," conceded Chairman Ted Stevens (R-Alaska) as his Senate Appropriations subcommittee on defense began marking up the Pentagon's $208 billion money bill yesterday. The full committee is slated to vote today on whether the B1 is worth the money. Sen. Patrick J. Leahy (R-Vt.), in releasing the CBO study, said, "I do not believe we can afford a $40 billion flying Edsel. The B1 bomber will be obsolete before it is deployed."

Sen. Ernest F. Hollings (D-S.C.), a member of the defense subcommittee and ranking Democrat on the Senate Budget Committee, said in an interview that given the deteriorating state of the national economy, "there's no way we can afford the B1 right now."

Stevens indicated, however, that he had been persuaded that the B1 is worth buying after all. Last week he had revealed that the CIA had told him in a secret briefing that the existing B52 would do as well as the proposed B1 bomber in penetrating the Soviet Union with cruise missiles between now and about 1995. Yesterday, however, Stevens said that the B1 "is an interim weapon that we must have to span a critical gulf in strategic superiority with the Soviet Union."

Defense Secretary Caspar W. Weinberger has handed lethal ammunition to Leahy, Hollings and other congressional critics of the B1 by testifying that the bomber would not be able to survive against Soviet defenses any later than 1990. Since the first B1 will not be ready until 1986, this has raised the question of whether it is worth it to pour billions into the B1 rather than wait a little longer for the radar-evading Stealth bomber now under development.

The Air Force has insisted that the B1 could penetrate the Soviet Union until 1995 and serve as a highly valuable cruise missile carrier and conventional bomber after that.

Gen. Lew Allen, Air Force chief of staff, said that the B52s must be replaced and the B1 is the only bomber in hand. He said the Stealth, although impressive, is still a bird in the bush.

Weinberger has told Congress the 100 B1s would cost $21 billion if the cost attributable to future inflation is subtracted. The price goes up to $28 billion if inflation is added, he said.

But the CBO and General Accounting Office contend that those estimates are misleading because they do not include the equipment that would have to be purchased to make the B1 a fighting machine. The CBO sifted through the GAO findings and arrived at the $39.8 billion price tag this way, not subtracting for inflation:

* $29.95 billion for the bare bomber.

* $1.43 billion to enlarge the rear bay of the plane and install a command link, racks for cruise missiles, and the electronics for firing them.

* $8.45 billion in the adjustments made by the GAO after examining Air Force estimates.

The Pentagon, queried last night, said it had not prepared a response to the CBO estimate.

Hollings said he would attempt in committee markup to delete money for the B1 on grounds it should be saved for the Stealth radar evader to be ready in the 1990s. Declaring the committee is closely divided on the B1, Hollings predicted the bomber would be shot down on the Senate floor.

Sen. Lowell P. Weicker (R-Conn.), another member of the defense appropriations subcommittee, said "the B1 will fly but the MX will not" in the Senate. The MX controversy centers on how Reagan intends to deploy the big land missile.

Reagan has recommended installing the first 36 to 40 MX missiles in existing Titan or Minuteman silos, or both. He would fortify the missiles by rebuilding the silos to withstand a nuclear blast.

Opponents contend that mobility, not more concrete, is the way to make the MX less vulnerable to accurate Soviet warheads than are existing missiles that stand in silos.

As in the case of the B1, the subcommittee yesterday decided to put off voting on MX funding until today's full committee meeting.

The subcommittee hopscotched from one Pentagon proposal to another yesterday before stopping for several minutes on the proposal to stop subsidizing cigarette sales in military post exchanges and commissaries.

Stevens complained that service people can buy cigarettes for $2 less a carton than they sell on the commercial market, thanks to an annual government subsidy of $96 million.

Given military pay raises and the fact that service people do not contribute to their retirement funds, "there's no excuse for subsidizing cigarettes at the PX," Stevens said.

Hollings disagreed, arguing that cut-rate cigarettes are considered a military benefit. Sen. Walter D. Huddleston (D-Ky.) contended it would be unfair to single out cigarettes, especially if liquor is sold on military bases at a low price.

Sen. Jake Garn (R-Utah), a Mormon, said of cigarettes and liquor: "Commissaries were set up for necessities. Cut them both out."

"Man doesn't live for bread alone," Huddleston replied.