Boston — Instead of plying the waters off Antarctica next year conducting underwater experiments, the 200-foot research ship Atlantis II will remain moored at the Woods Hole Oceanographic Institution on Cape Cod, enduring only the wavelets that lap at its hull.
Scientific research may be ''the foundation of progress,'' but cracks are starting to show in its supports. Huge federal deficits have forced government laboratories and private institutions that receive federal grants to share the cost of budget reductions.
So far, budget cuts have amounted to aslittle as 3 percent. But their effect is magnified by the fact that up to 80 percent of the expenses associated with many labs are fixed costs. So cuts in staff and in the use of equipment are the only means of saving money.
The Atlantis II is only one victim. At Brookhaven National Laboratory, Argonne National Laboratory, Fermi National Accelerator Laboratory, and other government research facilities, workers have been laid off and operating time for expensive machinery has been reduced.
There are approximately 200 federal research laboratories in the US with a combined budget of more than $5 billion. A number of these facilities, such as the national laboratories, are owned by the federal government. Others receive grants and contracts from agencies such as the National Science Foundation.
The national laboratories were established after World War II, primarily to continue atomic research, though their missions vary widely and involve such things as laser fusion and high energy physics. Over the years the focus of study at each laboratory has evolved to the point where some now are dealing with environmental and ecological research.
The Reagan administration currently is reviewing the role of the national laboratories in order to pinpoint areas where reform is needed.
The laboratories ''have done a lot of things that were not part of their original mission,'' says Stanley Schneider, assistant to the director of the White House Office of Science and Technology Policy. ''There are other things the labs could be doing and things they shouldn't be doing.''
Dr. James Kane, deputy director of the Department of Energy's Office of Energy Research, adds, ''This administration is trying to sort out what is truly legitimate research and what is politically induced.''
Some scientists laud the administration's stated concern for basic research and admit to the need for a review of the labs. But many others question the reasoning behind the budget-cutting policy.
''Basic research is vital to the stated goals of this administration - a strong economy and a strong national defense,'' says Dr. Leon Lederman, director of the Fermi National -Accelerator Laboratory.
Many researchers are quick to point out that the financial squeeze at government laboratories is not solely the result of the Reagan administration's economic policy. They put much of the blame on seven years of funding that has failed to match the rate of inflation. The result has been declining salaries, antiquated equipment, and a talent drain of young researchers.
''Geophysicists can double their salaries by going to an oil company,'' says Dr. Derek Spencer, associate director of research at the Woods Hole. ''But that is not entirely new. What is new is that they will also be working with better data.''
''We keep people because of the excitement in the field and, up until recently, the stability,'' adds Dr. Lederman. ''Because scientists can often collect greater salaries in private industry, even the threat of budget cuts causes concern.''
That threat lingers. On top of the belt tightening many laboratories had to endure last spring and summer, final budget figures for fiscal 1982 will not be released until January. ''The most difficult aspect of this is the total uncertainty surrounding the budget cuts,'' says Dr. Spencer. ''We don't know if we're facing severe cuts or no cuts.''
But even more than the size of the cuts, the abrupt nature in which they've been administered bothers many scientists.
''You can't have healthy scientific research on a stop-and-go basis,'' says William D. Carey, executive director of the American Association for the Advancement of Science. ''You don't handle (budget cuts) by turning the valve on and off. That's the most destructive thing you can do to research.''