The Republican-run Senate yesterday refused to weaken an anti-busing provision, and in the process suggested that Congress may move this year to take the government out of the school desegregation business almost entirely.

The Senate refused to defang a provision the House has passed barring the Justice Department from taking part in the future in any court case that might "directly or indirectly" lead to the busing of children beyond their neighborhood school to achieve desegregation.

Congress has already stripped the executive branch of its only other means of forcing desegregation where busing is required, which was to threaten to cut off the federal funds of offending school districts.

The anti--busing amendment was offered in the Senate by Jesse Helms R-N.C.) to the annual authorization bill for all the activities of the Justice Department.

Sen. Lowell P. Weicker (R-Conn.) has been conducting a one-man filibuster against the Helms proviso, and yesterday he moved to dilute it. His proposal said that nothing in the Helms amendment should be "interpreted to limit in any manner the Department of Justice in enforcing the Constitution of the United States."

This would have allowed the department to take part in busing suits, since most of these are intended to secure the constitutional rights of schoolchildren.

But the Senate, which has been debating the busing issue for four days, voted 45 to 30 against the Weicker proposal, and it appeared that if the 25 absentees had been present the vote would have been even more decisive.

Both Maryland senators voted with Weicker; boht Virginia senators voted with Helms. The Senate then quit for the weekend, leaving the issue technically unresolved, and will get back to it Monday.

Helms contends that busing has wasted taxpayers' money and gasoline without improving the quality of education. Weicker says Helms' intent is not simply to limit the generally unpopular remedy of forced busing, but to take the more drastic step of forbidding the Justice Department to file any suits dealing with school segregation because it could not know when doing so might "indirectly" lead to a court-issued busing order.

When the Senate resumes the debate Monday, Sen. J. Bennett Johnston (D-La.) may try to add to the Helms language a provision barring the federal courts from issuing busing orders which would carry students more than five miles or 15 minutes beyond the school closest to their homes.

The House has approved the Helms language as an amendment to its version of the Justice Department bill. The Senate now appears about to follow suit, and President Reagan is expected to sign it into law. President Carter vetoed such a provision last year on the grounds that it would interfere with the executive branch's duty to enforce the Constitution. Some opponents believe the courts would strike down the Helms' provision on similar grounds.

The Helms language would not stop private groups from filing busing suits; nor could it stop the courts from issuing busing orders on constitutional grounds.