CAMBRIDGE, Mass. (AP) _ At the same time the government is limiting research budgets it is failing to develop clear goals for how to spend the money, the presidents of Harvard and MIT said Tuesday.

''We must have a better sense of mission,'' said Charles Vest, president of the Massachusetts Institute of Technology.

Vest spoke at a conference, sponsored by Harvard University's John F. Kennedy School of Government, focusing on federal research and development policies.

Both Vest and Neil Rudenstine, president of Harvard, lamented how the government has shifted more research costs onto schools. This is seen in recent efforts to restrict how much universities bill the government for indirect costs, such as general library and utility expenses.

''We're beginning to think of university research as a commodity to be procured by the government,'' Vest said.

Rudenstine said part of the problem is that with the United States not at war or facing a military threat from the Soviet Union there is disagreement over what research is important.

''We don't have the same kind of national consensus,'' he said.

Furthermore, Rudenstine said, ''our resources are no longer coming out of our ears. We're in a much more scarce period.''

But the energy once devoted to military research could be redirected, to such things as health care and the environment, he said.

Rudenstine also said universities must get better at articulating the importance of basic research for developing future technologies, even when there appears to be no immediate payoff.

Walter Massey, director of the National Science Foundation, agreed that without the ''national security umbrella, we do need a new rhetoric.''

The fundamental reason for research is to ''improve the quality of living of our citizens,'' Massey said, but he added that can be hard to sell politically.

In the meantime, universities shouldn't expect rapid increases in government spending for research, given the strained federal budget, Massey said. He urged schools and industries to cooperate more on research so they can use their resources more efficiently.

U.S. Rep. Joseph P. Kennedy II, D-Mass., proposed creating a new office within the U.S. Environmental Protection Agency to channel money to the private sector for environmental research and development.

Kennedy said such a program would help the country advance energy conservation, waste recycling and pollution cleanup, while creating jobs based on that new technology.