Boston — Having weathered a two-year controversy over its future, the sprawling national laboratory system is on the rebound. A White House Science Council report last year listed ''serious deficiencies'' in the 700 federally funded labs and suggested ways to correct them. This week, however, a followup report presented to President Reagan cites substantial progress toward meeting the report's recommendations.
''Things have really come around,'' says David Packard, author of last year's report and chairman of Hewlett-Packard Corporation. ''The funding agencies are becoming more flexible, the labs are thinking their programs over very carefully.''
They've had to. Virtually no one challenged the labs' traditional preeminence in American research and development since their establishment after World War II. They had made large contributions to the nation's nuclear power industry and weapons arsenal. They pioneered the use of radioisotopes in nuclear medicine. Efforts at some facilities had spawned Nobel-prize-winning discoveries.
But for the past few years, the labs - from a three-man outpost in Maine to massive research complexes in California - have been fighting a multifront war. Budget cuts and competition for technical personnel from some lavishly funded university programs and industry have siphoned off top researchers. Meanwhile, several government investigations of the laboratory program questioned its purpose. They charged that a growth spurt in the 1970s had left the largest labs flabby and directionless. White House science officers said much of the labs' research would be better left to the private sector. Some critics called the labs obsolete.
The worst seems to be over - for now. Employee rolls have been pared and priorities reordered among the largest labs. Red tape has been cut. New partnerships with industry have been established. The critics aren't so noisy.
''We're certainly leaner,'' says Herman Postma, director of the Oak Ridge National Laboratory. Budget cuts forced Oak Ridge to reduce its staff of 5,400 by 700 last year. ''I'd also say we were better prepared to carry out our mission of doing long-term, high-risk basic research.''
For example, the council's report complained that many labs did not have clearly defined missions. So the Department of Energy now requires that the 57 labs it funds each draw up five-year plans detailing research projects, goals, and budgets, and has set up a committee to oversee them.
Directors of the labs also have more control over their funds, the report says. Up to 1 percent of the laboratories' budgets is ''exploratory funds,'' to be spent at the director's discretion.
Details are also being ironed out on an extensive research agreement between US Steel and two of the big, multipurpose labs at Argonne, Ill., and Oak Ridge. The agreement is the first of several expected to help muffle criticism, echoed in the White House report, that the labs have been isolated from the private sector.
But the path to reform is still strewn with some obstacles. Expected to cause much controversy is a proposal to free government-operated labs from the civil-service pay scale. By creating a separate pay scale for scientists and technicians and establishing promotions based on merit as well as seniority, the labs hope to be better equipped to compete with the financial lures from industry.
Proponents of the idea expect vociferous opposition from the civil service. ''We won't get everything we want, of course,'' says Mr. Packard. ''That's politics.''
And politics is what still concerns lab officials, particularly as reflected in the uncertainties of congressional funding. ''You just can't run a first-class research operation unless you can plan ahead,'' says Alan Schreishein, director of the Argonne national laboratory.
A Packard proposal favored by lab administrations would establish a two- or three-year rolling budget instead of the current annual review. It seems unlikely to materialize anytime soon.
Some lab officials are concerned that as Congress's post-election attention turns to reducing the US budget deficit, another round of funding cuts could bring some of the biggest labs down below the ''critical mass'' size needed to do many types of research.
''I think its going to be a race between the next round of budget cuts and another energy crisis,'' says Dr. Postma. The labs saw their period of greatest growth during the 1973 Arab oil embargo, as the country scrambled to find alternative energy sources. ''There is a relative sigh of relief that we're not where we were two years ago - but we're not breathing easily yet.''