The nation's savings and loans continued to pile up big losses in 1990, but analysts say lower interest rates and the government's program of closing and rescuing failed institutions could lead to improvement this year.

The 2,342 thrifts still outside government control at the end of the year lost $965 million in the final three months of 1990, the Office of Thrift Supervision said Thursday. For the entire year, private-sector thrifts lost $2.41 billion.The 1990 loss was down from $6.23 billion in 1989, largely because of the removal of 213 failed institutions by the government bailout agency, the Resolution Trust Corp.

However, losses rose 25 percent from the third to fourth quarters, even with the seizure of 39 insolvent S&Ls those months.

Also - and despite the removal of the worst thrifts - private-sector S&Ls' bad loans as a percentage of all loans rose through the year. The percentage of bad loans in S&L portfolios was 2.34 at the end of the year, compared with 2.03 at the end of the first quarter.

The industry as a whole has not earned money since 1986.

Economist Martin Regalia of the National Council of Savings Institutions said the latest data seem to show that the losses were connected with the economy and were not a reflection of huge thrift problems built up during the 1980s.

"What this means is that once the RTC is done shutting down thrifts, once the economy picks up, we may start to see improvement," he said.

Thrift Office Director Timothy Ryan, however, was unwilling to predict immediate improvement.

"We are uncertain at this time what to expect in the first quarter of 1991, especially in view of the economic slowdown and weak real estate market," he said.

Regalia and other private analysts attributed the industry's continuing problems to the national recession, to the deterioration of real estate markets, particularly in the Northeast, and to the housing industry's slowdown.

Construction and sales of new homes slumped in 1990 to the lowest point since the recession of 1982. Existing home sales fell to a five-year low.