In what has become an increasingly familiar exercise in brinksmanship, most of the federal bureaucracy is preparing again for a possible shutdown when the fiscal year expires at midnight Friday, and some agencies could go out of business unless Congress rescues them.

Throughout the government, however, officials are treating the prospect that their money will run out--unless Congress passes a stopgap funding measure to carry them beyond Oct. 1--as something less than a calamity.

"We are old hands at this," said Neal Friedman, spokesman for the Federal Trade Commission, which has endured brief shutdowns seven times in the past three years. "They just pull a standard memo out of the files and put a new date on it."

The atmosphere is more serious at several agencies that theoretically could go out of business if their authorizations are not extended beyond fiscal 1983.

At the Civil Rights Commission, for example, congressional debate on the terms of its extension is closely entwined with a dispute over President Reagan's move to replace three commissioners with his own nominees.

Most observers expect Congress to adopt a last-minute bill extending current funding levels for 45 days. That measure is more important than it seems because many agencies have had to live with temporary funding levels for an entire fiscal year.

"The continuing resolution has become an omnibus appropriations bill, because Congress has no intention of coming back to fund some of these individual agencies," said Edwin L. Dale Jr., spokesman for the Office of Management and Budget. "The last continuing resolution was 500 pages long."

A House subcommittee has estimated that a one-day government shutdown in November, 1981, cost $85 million in salaries paid to employes who were doing work related to the shutdown, rather than their regular jobs.

This time, four fiscal 1984 appropriations bills, including those covering the Transportation and Housing and Urban Development departments, Veterans Administration and Environmental Protection Agency, already have been passed. Those agencies would not be affected.

The rest of the government is making contingency plans to start winding down on Monday, except for exempt employes such as members of the military and Coast Guard, diplomats and air traffic controllers.

At the Federal Trade Commission, for example, employes had to check whether Chairman James C. Miller III would have to pay his way when he returns from a trip to California late Friday. The answer: the agency will pay, but Miller can't extend his trip if the government shuts down.

A congressional battle also is brewing over important changes in the FTC's reauthorization bill. Some senators want to restrict the commission's authority to regulate doctors' and lawyers' business practices. Others want to give Congress a two-house legislative veto over new FTC regulations, replacing the one-house veto that was used to overturn such controversial rules as those regulating used-car dealers before the one-house veto was struck down by the Supreme Court.

A vote expected today on Reagan's three Civil Rights Commission nominees could determine whether the commission loses its authorization and has to go through the motions of shutting down.

Sen. Arlen Specter (R-Pa.) is pushing a compromise in the Judiciary Committee that would give commission members fixed, six-year terms, which would allow Reagan to replace only one member now. There are competing proposals to expand the panel from six to eight members.

Some agencies can carry on without an authorization, as long as Congress provides money. Officials at the Office of Government Ethics, whose five-year authorization expires Saturday, say they could continue because they are a sub-unit of the Office of Personnel Management.

HUD, like some other Cabinet departments, has managed to spend money without an authorization bill for three years, but it has been blocked from adding new programs. This means there will be little new construction of subsidized housing, which the administration opposes, but also no action on such HUD initiatives as housing "vouchers" for the poor and grants to renovate rental properties.

One change that definitely will take effect Saturday is new rules governing about $44 billion in Medicare payments to hospitals. Over three years, the nation's 7,000 hospitals must convert to a "prospective payment" system in which they will be paid in advance according to 467 separate diagnostic categories, ranging from cataracts to gall bladder surgery.

Beginning this weekend, nearly a quarter of the hospitals must start to live within these fixed limits or absorb the difference.

Other Medicare rules will restrict overlapping billings by hospital-based pathologists, radiologists and anesthesiolgists and their facilities for the same lab tests.

The Export Administration Act, which allows the president to restrict exports for reasons of national security or foreign policy, also expires Saturday.

House and Senate factions have been arguing about whether to relax or tighten the controls. A Commerce Department official said he is not sure whether Reagan can use emergency powers to bar exports if the law is allowed to lapse.

Nearly all funds run out Saturday for the controversial Clinch River breeder reactor in Tennessee. An Energy Department spokesman said work on the nuclear reactor could stop within two weeks unless Congress, which has come closer to killing the project each year, votes new money for it.