The Federal Home Loan Bank Board has issued a clarification of its rules in an effort to prevent federally chartered savings and loan associations from refusing to accept overdue mortgage payments that do not include late charges. The ruling also prohibits S&Ls from adding late charges to the loan's principal balance.

Although these practices have been specifically outlawed by federal regulations since 1976, they are still widespread, a FHLBB spokeswoman said.

Some S&Ls use the threat of not accepting principal and interest payments as a way to force customers to pay late charges when these charges may be in dispute, the agency said. Very rarely - presumably in marginal or persistant deadbeat cases or where the loan has become unprofitable - an S&L, might use this tactic to force foreclosure. Others use this as a way to increase profits on loans by adding the charges to the balance due, the board said. Consumer complaints as well as industry inquiries about the practice led to a clarification by Robert J. Moore, deputy director of the FHLBB's Office of Examinations and Supervision.

"Repayment of a loan," Moore wrote, "is measured in terms of making the required payments, rather than in terms of collecting late charges." He did, however, acknowledge that there was a problem with deadbeats."If untimely payment persists, action can be instituted when the aggregate amount involved becomes significant," he said.

By this he meant that if late charges have not been paid by the time the loan matures, the association could take the borrower to court. The S&L would also have a chance to recoup its late charges if the house were sold before the mortgage were paid off.