Gen. George S. Brown told Congress yesterday that President Carter's plan to withdraw all U.S. troops from South Korea was in conflict with the Joint Chiefs of Staff "in a fundamental way" but that the apprehensions of the top military commanders were taken into account in the final program.

Brown, chairman of the Joint Chiefs, said the armed service heads still regard the withdrawal as "an additional risk - but an acceptable risk."

He told reporters after testifying before the House Armed Services Investigations Subcommittee that North Korea's shooting down of an Army helicopter on Thursday morning (Wednesday night in Washington) was "an accident" that does not alter the chiefs' support of the President's withdrawal plan.

"I think the airman strayed off course," said Brown. "I don't know of an American airman who has flown deliberately into interment. I think this incident will have no impact on the planned withdrawal."

In lengthy and often testy exchanges between Brown and subcommittee Chairman Samuel S. Stratton (D-N.Y.), the Joint Chiefs chairman confirmed that in March his staff submitted "an option" to limit the withdrawal from South Korea to 7,000 troops between now and 1982.

"It is accurate to say judgment well against the chiefs in a fundamental way," Brown said. But he added that "we certainly accept" the President's withdrawal plan as announced on May 26 because it includes the military help for South Korea recommended by the chiefs.

Carter said the United States will leave in South Korea "adequate intelligence forces, observation forces, air forces, naval forces and a firm, open treaty . . ."

Brown said withdrawing the Army's 2d Division from South Korea and restationing it in the United States will not save any money, partly because much equipment will be left for the South Koreans.

"It's going to cost more money," Brown said of the withdrawal, when the extra military assistance is counted. "But when we left forces in 1950" in South Korea, he added, "I did not expect them to be there forever, I welcome this initiative" by the President to make South Korea more self-reliant.

"We have been unfair to the Republic of Korea," Brown said, "because they have leaned on us militarily" instead of taking over from Americans such activities as planning, supplying forces and gathering intelligence.

Although "the likelihood of this withdrawal program leading to war was perhaps slightly higher" than leaving American ground troops in Korea, "we don't believe war is going to come because of it," he said.

The chiefs are assuming that the withdrawals will be assessed as they proceed, he added. Any time the chiefs conclude that the withdrawals are imperiling national security, 'the Joint Chiefs of Staff would be negligent if they didn't stand up' and recommend that the program to be "readjusted," he said.

Even with the planned withdrawals, Brown said, the United States will still have a powerful military presence in the Pacific, including Marines in Okinawa and Japan available to back up South Korean troops.

"We have the resources," Brown said. "Whether we have the political will, I can't judge."

"Were you muted by the President!" when it came to the chiefs' commenting on Carter's withdrawal plan" asked Rep. Ronald V. Dellums (D-Claif.).

"No, Mr. Dellums," Brown responded, "We were free and frank and candid and our views were sought."

Stratton and Brown argued back and forth over whether the subcommittee should have access to "back channel" messages between the chiefs and field commanders on Carter's withdrawal plan.

After protesting that back channel teletype messages and letters were like personal letters and should not be put under congressional scrutiny Brown agreed to let a committee staffer look through the withdrawal plan traffic and request copies.

If Brown concludes that a requested copy should not be supplied, he said he would pass that option up the chain of command to Defense Secretary Harold Brown and let him decide the question.