A federal judge has denied a request by the U.S. Equal Employment Opportunity Commission for a preliminary injunction against Howard University in a discrimination case, saying there is "no evidence whatsoever . . . that the university was intimidating or threatening" potential witnesses.

U.S. District Judge Thomas A. Flannery said that even though several university employes said they feared reprisals by the school if they spoke to EEOC investigators, affidavits indicated that "no one at Howard University had ever threatened them or in any way discouraged them from cooperating" with the investigation.

The case involves a sex discrimination complaint against the university filed with the EEOC last fall by Michael A. Harris, a former Howard lawyer who said favored treatment was given to women in the university's office of legal counsel. Harris was fired from the counsel's office on Jan. 31, and he subsequently contended that his dismissal occurred because he had made his original complaint.

In its request for an injunction, the EEOC asked that the university be barred from any action to discourage employes from helping its investigation of the Harris case. It also asked that Harris be reinstated to his $29,000-a-year job.

Flannery turned down both requests. He said there was "a climate of fear at Howard University," but no evidence "of actions on the part of Howard University to create that climate."

He said any reinstatement of Harris should await the outcome of the EEOC investigation or later court action.

Earl Harper, regional attorney in the commission's Baltimore office, said yesterday that the agency's investigation would continue "even though we don't have the protection of the court." Harper said the EEOC had not decided yet whether to appeal Flannery's ruling.

Lawyers for Howard could not be reached for comment. The university had earlier denied that Harris suffered any discrimination.

Last winter the case, which received prominent coverage in The Hilltop campus newspaper, was at the center of major student demonstrations against university President James Cheek.

The student editor of the paper, Janice McKnight, was expelled from school the day after Harris was fired on the grounds that she had falsified information on her admissions application in 1979.

McKnight was reinstated, but several weeks later the paper was suspended for the rest of the term because officials said it had run out of funds.