America's major research universities fear that new points of tension may be straining their long-uneasy partnership with the federal government, the prime source of college research money.

The tension, according to university presidents who met here this week, is caused by budget cuts for higher education, proposals to revamp the tax code that could discourage large private donations, and stricter accounting rules from the Office of Management and Budget that have made colleges bear more of the cost of federally sponsored research.

"All these different points converge" on college campuses, said Robert M. Rosenzweig, president of the Association of American Universities (AAU). "There's no other place where the totality of the effect of different initiatives can be taken account of."

Universities and the government have always viewed each other with suspicion, despite a mutually dependent relationship involving research grants and contracts.

The government needs the schools to supply expertise and conduct most of its basic research -- a need that has grown even more intense with the Reagan administration's emphasis on the ambitious space-based Strategic Defense Initiative, also known as "Star Wars." The campuses, while dependent on government funds, are wary of being drawn into too close a relationship -- particularly on a controversial project like Star Wars. Universities have long viewed the government, with its demands for secrecy, as the main threat to their cherished academic freedom.

The latest points of tension, however, are budgetary. The university presidents who gathered here said that various unrelated government policies had the cumulative effect of impairing the large research schools in fulfilling what they termed their "national mission."

Peter McGrath, president of the University of Missouri, said the decline in federal support for graduate student fellowships and training grants under the Reagan administration has led to a "national crisis" in graduate education, with most science- and math-related graduate courses now populated largely by foreign nationals.

McGrath said foreign students now account for more than 40 percent of all graduate students in engineering schools, 40 percent of the graduate population in math and almost 40 percent in computer science.

Regarding the tax code, Harvard President Derek Bok said proposed changes would "diminish the incentive to give," a potentially serious threat to private schools such as his that depend in large measure on gifts from wealthy donors.

Bok said while it is true that universities' endowments have increased with the rebounding of the stock market under the Reagan administration, "vast accumulated backlogs of deferred maintenance" can easily drain any increases. Reduced federal funding for higher education, coming at a time when tax changes could reduce donations, amounts to "a pincer movement," Bok said.

Stanford University President Donald Kennedy expressed fears -- also voiced by many other college presidents recently -- that proposed changes in OMB accounting regulations will reduce the amount of research overhead the schools can be reimbursed for.

Those overhead costs have been a sore point, with aggressive auditors forcing some schools to pay back money to the government when disputes arise over bookkeeping. Kennedy said the new regulations, due to take effect in July, could cost universities $100 million a year.