Palo Alto, Calif. — ''You built the knowledge base that made the changes now taking place in Washington possible.'' Franklin D. Roosevelt to members of his New Deal ''brain trust''? Or John F. Kennedy to the two-score Harvard University scholars who helped shape the New Frontier?
No. The words were addressed by Ronald Reagan to the overseers of Stanford University's Hoover Institution on War, Revolution, and Peace. The occasion was a White House reception in January 1982, just a year after President Reagan initiated his own conservative revolution in Washington.
Now Mr. Reagan's praise is being turned against the institute established by Herbert Hoover in 1919 and built on the unique materials he collected in a career of distinguished service to the United States and the world. It is cited by critics as an indication that the institute has become, in the words of one, ''a political and partisan organization.''
On the basis of that charge - and others alleging that the Hoover Institution has too much influence on faculty appointments and has amassed too much money and power - the Stanford faculty senate passed a resolution May 26. It urged university president Donald Kennedy ''to consult with the board of trustees with a view to appointing a committee in the near future to explore and reassess the relations between the Hoover Institution and the university, with the goal of promoting more effective and cooperative relations.''
Dr. Kennedy has indicated that such a panel will be recommended to the trustess in the fall.
Dr. Glenn Campbell, director of the institute since being chosen by Herbert Hoover in 1959, is as unwavering in his pride over Reagan's praise as he is in his conviction that any ''reassessment'' will only confirm the institution's value to Stanford and the nation. He also asserts that the phrase ''explore and reassess'' in the faculty resolution replaced the wording of a petition presented by 50 faculty members urging ''an immediate and independent inquiry including a public report.''
The faculty senate, the plain-spoken Dr. Campbell says, ''threw the petitioners a bone.''
Aside from the ''local'' aspects of the controversy at Stanford - which unsurprisingly include elements of campus politics as well as legitimate concerns - is its relevance to a little-publicized, but quietly increasing debate over two matters affecting the character of higher education in the United States: (1) the growing number and influence of ''institutes'' affiliated with colleges and universities; (2) the relationship between academia and such ''outside'' entities as businesses, government, and political parties.
Prof. John Manley of Stanford's political science department, a leader of the present attack on the Hoover Institution, voices a concern expressed by academicians on other campuses when he says the university may be in danger of losing its ''reputation and legitimacy among the American public'' if it appears to have compromised ''the values of objectivity, nonpartisanship, and the nonpolitical search for knowledge.''
In the past, however, this concern has been raised almost entirely in connection with relationships between academicians and industries - acceptance of research grants, consulting, entrepreneurial arrangements, and the financing by private business of certain research facilities.
Dr. Kennedy is not only familiar with these issues, but he has also been prominent in probing them. The Stanford president was host, in March 1982, at a conference of university officials and business executives which examined the role of industry in university research. He has also testified at length before congressional committees.
But whether involved with corporations seeking profits or with institutes that might be serving private or partisan ends, colleges and universities are being warned to weigh the risks and guard against erosion of academic freedom.
Hoover Institution spokesmen and research fellows point out that the cry of ''partisanship'' was not heard from the left until a conservative US president began drawing both personnel and ideas from a think tank with a reputed conservative orientation.
The Hoover Tower has been the dominant Stanford landmark since it was built in the early 1940s as the repository for the former president's personal papers and a wealth of other materials. The institution it symbolizes is just as dominant in Stanford's intellectual life.
The Hoover is a magnet for scholars from all over the world as well as a key resource for Stanford students.
The institution has provided consultation, research, and personnel for most presidential administrations, Democratic and Republican, in the last few decades. But the Reagan-Hoover tie has dramatically illustrated two significant changes in America - the shift of political power from the East Coast to the West Coast and the rising in the West of an intellectual establishment that appears to have challenged the dominance of the ''Eastern liberal establishment'' in affairs of state.
Since ''conservatism'' is a major element in both the political orientation and the intellectual atmosphere of the West, the shift in power and influence may well disquiet those who identify with the ''old order'' of the ''liberal'' East.
In response to charges of a conservative political bias on the part of the Hoover Institution, three senior research fellows currently in residence - Peter Duignan, Lewis H. Gann, and Milorad Drachkovitch - wrote an article in the May 18 ''Campus Report,'' in which they asserted: ''Hoover has balance and is open, tolerant, and free of partisanship. Furthermore, Hoover scholars are at least as divided on political issues as their colleagues in the university.''
But perhaps the most impressive testimonial elicited by the current controversy was addressed to Stanford's Kennedy by senior research fellow Sidney Hook, New York University professor emeritus of philosophy. Identifying himself as ''a lifelong socialist'' and current member of Social-Democrats, USA, Dr. Hook said his 10 years in residence at Hoover ''have been productive (and) intellectually stimulating'' primarily because of ''the continued challenge to my positions, the give and take with varied points of view. . . .
''To single out Hoover for investigation because of the presence of some outstanding conservative thinkers among its fellows could very well establish a precedent for investigation of other disciplines and departments at Stanford University because of the absence of conservative thinkers among them. Where the life of the mind is concerned, such political epithets are irrelevant.''