The Federal Home Loan Bank Board yesterday announced that it has made the first exception to its 10-year-old policy of prohibiting savins and loan associations from setting up branches in states other than the one in which they are chartered.

While federal law prohibits domestic banks from having branches elsewhere than their home state, there is no such law prohibiting interstate branching by savings and loan associations.

Since 1967, however, the Federal Home Loan Bank Board, which regulates federally chartered S&Ls, has prohibited interstate branches.

Federal Home Loan Bank Board chairman Garth Marston insisted that the decision, reached Wednesday but not announced until late yesterday afternoon, does not set a precedent.

He said there were "unique, unusual and special circumstances involved which allowed the board to approve the charter federal branch without changing its general policy, or making a general exception to its general policy."

Nonetheless, the decision can be expected to upset bankers already concerned about growing competition from specialized savings institutions such as S&Ls, mutual savings banks and credit unions.

What the bank board approved yesterday was the application of a small Georgia-based S&L to set up a branch two-and-a-half miles from its home office across the line in Alabama.

The Alabama legislature two years ago passed a law, Marston said, which invited the Georgia S&L, Charter Federal Savings and Loan, to establish a branch office at the location in question.

The Georgia S&L is located in West Point, Ga. The approved branch is in Chambers County, Alabama.

Marston said that the bank board would not amend its general prohibition against interstate branching for either the entire industry or a segment of it without "first going through public notice-and-comment rulemaking proceedings."

He also said that Wednesday's decision should not "be construed as a 'signal' that the board has decided to submit for public comment" such as proposal.

Some federally S&Ls do maintain branches in more than one state, but those were interested branches that were already established before the bank board's policy was announced. No new interstate branches have been permitted since 1967.