When Congress returns next week it will find an urgent supplemental appropriations bill waiting for it to bail out four agencies: the U.S. Customs Service, which wants an extra $3.4 million; the Merit Systems Protection Board, $4 million; the U.S. Tax Court, $1.5 million, and the Treasury Department's Bureau of Alcohol, Tobacco and Firearms, $15.7 million. The bill also includes a request for $81.6 million for the Bureau of Government Financial Operations, but that is because of a change in accounting methods, not because of a lack of funds.

The agencies are funded through the Treasury, Postal Service and general government appropriations bill that has been stymied this year by attempts to tack a controversial anti-abortion amendment onto it. Since December, the agencies have been operating under a continuing resolution that cut their fiscal 1982 budgets by 16 percent.

The agencies have been in trouble ever since. The Tax Court has threatened to stop holding hearings, and the merit systems board, which was trying to resolve 11,000 air traffic controller cases, called the budget cuts impossible.

Congress is expected to approve funding for three of the agencies without much trouble, but the BATF, which may be going out of business anyway, may not be as lucky. One House committee already has said it doesn't believe BATF's situation is critical. About a dozen other agencies caught in the crunch won't get any help this time out.