The nation's savings and loans lost a record $12.1 billion in 1988 and face continuing problems in 1989 from rising interest rates, the government reports.

The Federal Home Loan Bank Board said the 2,949 S&Ls lost $2.3 billion in the fourth quarter, pushing red ink for the year well past the previous record of $7.8 billion set in 1987.Still, losses in the second half of the year, $4.1 billion, were down substantially from the first half's $8 billion, largely because of government efforts to close, merge or prop up 223 institutions, also a post-Depression record.

James Barth, chief economist of the bank board, said the worst may be over, but he warned that the effect of rising interest rates in 1989 will be "obviously adverse."

"Operating income should be lower across the board for all thrifts in the first and second quarters," he said, but he also added, "I would guess we aren't going to see $12.1 billion (in losses) in 1989."