Interior Secretary James G. Watt is not the only Cabinet member in the Reagan administration who has used the Republican National Committee to perform political loyalty checks on his advisory boards.

The Agriculture Department systematically checked party affiliations of science advisers with the RNC until the practice came under fire last year. The Education Department still performs such checks. So does the White House personnel office.

RNC Chairman Frank J. Fahrenkopf Jr. said he believes that all but three federal departments--State, Justice and Defense--routinely call the GOP committee to check the political stripe of scientists and non-scientists who are candidates for government advisory boards.

"We do not say yes or no on the appointment," Fahrenkopf said. "If we can get qualified Republicans, I'm for it."

All modern administrations have used appointments to advisory boards as patronage plums. Former Democratic National Committee chairman John C. White said he was frustrated that the Carter White House did not use them more often.

"We weren't that well organized," White said, almost ruefully. "I would find out occasionally when a vacancy occurred and try to influence it, but I had a spectacular lack of success."

But the Reagan administration apparently has gone further than its predecessors did in putting scientists through the same screening process as candidates for general policy advisory boards. The practice has come under increasing fire from scientists who argue that it taints them and hinders the search for objective advice.

"I cannot recall a period when political clearances of scientific panels and commissions was a practice to the extent it is now," said William Carey, executive director of the American Association for the Advancement of Science, the nation's largest organization of scientists. "When you use this kind of system for technical advice, which is needed for good regulatory policy, then it's going too far."

Carey was a budget official in the Kennedy and Johnson administrations.

"As a scientist, I am concerned that this process will certainly hinder the level of advice the government gets," said Donald Boesch, director of the marine sciences program for Louisiana universities.

Boesch, a registered Independent, was one of 10 scientists removed from Watt's advisory board on offshore oil after their names were submitted to the RNC for a check of their party affiliations. The RNC wrote "no" by the 10 names and "yes" by four others, and returned the list to Watt.

Boesch said he was told by Interior officials that he should seek backing from Gov. David C. Treen (R-La.) in order to save his spot on the panel. He said Treen later wrote him a letter of recommendation, but he was removed anyway.

Fahrenkopf stressed that not all Cabinet secretaries apply the political litmus test as rigorously as Watt, and that the RNC provides the information only on an agency's request.

The White House put distance between itself and Watt's approach this week when spokesman Larry Speakes said that President Reagan believes "scientific advisory groups should call on the best scientific minds regardless of party affiliation or political persuasion."

The Agriculture Department last year performed political checks on candidates for a board of agricultural research scientists that advises the agency on the quality of applications for about $16 million in research grants, according James Handley, special assistant to Agriculture Secretary John R. Block.

An aide to Block said the practice was discontinued after it came under fire. He said Block now submits all nominees for scientific and other advisory boards to the White House personnel office.

Watt's offshore oil board, like the Agriculture panel, was limited strictly to scientific matters, not policy. Its charter limits it to advising the agency on how to improve the scientific quality of studies of the environmental impact of offshore drilling.

Many of the federal government's 948 advisory boards do make policy suggestions, however, and it was changes in the makeup of such panels at the Environmental Protection Agency that raised questions about the influence of politics on the advice the government was receiving on scientific matters.

The EPA in the last two years removed more than 50 scientists from its technical advisory boards after conservative groups provided lists classifying them as "horrible," "a real activist" or "a Nader on toxics." EPA officials said the tests at their agency were generally more ideological than political.

At the Food and Drug Administration, officials said that political appointees attempted to influence the selection of a panel of science advisers for government policies on vaccines. But they backed off, the officials said, after FDA civil servants argued that the political appointees' candidates were not well qualified.

These officials said that the Carter administration occasionally made political checks on appointees to scientific panels, although the system was not centralized through the Democratic National Committee.

In the area of non-scientific panels, the Reagan administration has been candid about its efforts to put Republicans on even the most obscure boards. Lyn Nofziger, former White House political director, argued strenuously for more such appointments when he was a presidential aide.

"Always fire the opposition and bring in your own people," said Nofziger, now a private consultant. "I'm a great believer in the spoils system."

Of the 948 federal government advisory boards, some are appointed by the president and some by Cabinet secretaries or senior agency officials. Federal law says that the panels must be "fairly balanced," but does not specifically require them to be bipartisan.

At the Education Department, a senior official said the party affiliations of all nominees to advisory boards are checked with the RNC, as "just one of the bits of information we use in considering an appointee."

Sources said that the White House personnel office recently checked the political affiliation of an Indiana University history professor who had been nominated for a post on the National Archives Advisory Council. Allan Bogue, president of the organization, said this was the first time he knew of such a check being made.

A White House official said party affiliations of all candidates for presidential appointments are checked through the RNC, which consults state GOP chairmen.

The RNC official who devised the system of checking party affiliations was Fred Biebel, a deputy to former chairman Richard Richards. White House officials were not always pleased with Biebel's vigorous efforts to place Republicans on advisory boards, and in late 1981 tried to restrain him from influencing appointments on a number of minor panels, a senior administration official said.