The nation's savings institutions lost $19.9 billion in deposits during the first two months of 1990, nearly matching the record outflows in the same period a year earlier, the government said yesterday.

Depositors at institutions still under private ownership withdrew $13.7 billion more than they deposited during January and February, the Treasury Department's Office of Thrift Supervision said in a long-delayed statistical report. Account holders at failed institutions under government control withdrew a net $6.2 billion.

At all institutions, net withdrawals totaled $13.3 billion in January, a record topping the previous mark of $10.9 billion in January 1989 and $6.6 billion in February.

The two-month total fell just short of the $20 billion drain in January-February 1989. February marked the 20th deposit drain in 21 months and left the industry's total deposit base at $926.5 billion.

Economists attributed the outflow to three factors:

Deliberate shrinkage by solvent S&Ls trying to meet stringent capital requirements imposed by last August's bailout bill.

A cut in the high interest rates offered by failed institutions after they come under government control.

Lingering confidence problems among depositors at failed thrifts, despite government insurance guaranteeing each account up to $100,000.

Yesterday's report was the first 1990 data released for thrifts. Computer problems and disarray caused by the reorganization of the S&L bureaucracy delayed the reports.