Two prestigious universities have accused the Defense Department of misrepresenting their roles in Strategic Defense Initiative research projects in an effort to help sell the program to Congress.

The Pentagon's Strategic Defense Initiative (SDI) Organization has said in a series of press releases since February that it has formed four "consortiums" of universities to research technical aspects of President Reagan's proposed space-based missile defense system, known as "Star Wars."

But two of the universities -- the Massachusetts Institute of Technology (MIT) and the California Institute of Technology (Caltech) -- said the Defense Department has lined up individual researchers at their schools and not the institutes themselves.

In a May 3 letter to SDIO Director Lt. Gen. James A. Abrahamson, Caltech President Marvin Goldberger complained of "gross misrepresentation" and accused officials of making "manifestly false" statements to the press implying university commitment to the program.

MIT President Paul Gray, in his commencement speech Monday, said the Pentagon is engaged in a "manipulative effort to garner implicit institutional endorsement for SDI" to strengthen the bid for congressional funds.

"What I find particularly troublesome about SDI funding is the effort to short-circuit the debate and use MIT and other universities as political instruments," Gray told the graduating class. "This university will not be used. Any participation at MIT in SDI-funded research should in no way be understood or used as an institutional endorsement of the SDI program."

A spokesman for the SDI office denied any intention to misrepresent the universities' role and said, "We're not using anyone. All we're trying to do is find the best scientific minds."

The dispute occurred as the administration struggles with Congress over funding of SDI research and fends off criticism of the program by part of the scientific community.

The issue has divided many academic institutions.

What angered Goldberger was an April 24 news release from the SDI office naming a consortium of universities, including Caltech, to study "new and innovative techniques for high-speed computing using optical signal processing."

Dennis Meredith, Caltech's spokesman, said an assistant professor of electrical engineering who specializes in optical computing had received a $50,000 grant to work on the research project for six months.

But he had received the grant from the University of Dayton Research Institute, a subcontractor for the SDI office, Meredith said, and the Caltech faculty committee that approved the research proposal early this spring "wasn't aware of [an] SDI connection."

"Listing Caltech as a part of a consortium implies it's involved in a major effort on SDI," Meredith said. "But Caltech wasn't even involved in any discussion on research. There's no institutional commitment."

In a telephone interview, Gray said the same press release included MIT's Lincoln Laboratory even though "the first time we learned we were in a consortium was when we read it in the newspaper. You'd think if an organization was going to be drawn into a consortium, the discussions would involve more than one researcher.

"It's manipulation that tries to use the reputation of MIT to lend credibility to that [SDI] undertaking," he said.

The SDI spokesman said future announcements of consortiums will focus on researchers instead of their universities, she said.