The president of the University of Minnesota said yesterday that the NCAA is a "protected monopoly" ruling colleges by "intimidation and threats of reprisal" and operates a judicial system "nothing short of a sham."

C. Peter Magrath, a political scientist and former professor of constitutional law detailed for the House Subcommittee on Oversight and Investigations the many legal battles his university has had with the NCAA over the past few years.

While stressing he was not defending the "unsportsmanlike conduct" that led to the filing of 112 violations against Minnesota, Magrath and Minnesota Vice President Stanley B. Kelger said the NCAA seemed more intent on punishing schools than correcting whatever problems existed.

Because of his experiences challenging the NCAA both in and out of court, Magrath said, he is apprehensive the school might be placed on a NCAA "enemies list" in the next few years.

This remark and others during the third day of hearings on the NCAA's enforcement procedures, prompted John E. Moss (D-Calif.), subcommittee chairman, to warn he would turn over any evidence of intimidation of witnesses by the NCAA to the Justice Department.

Thomas C. Hansen, assistant executive director of the NCAA, said of Magrath's remarks, "I think that is totally, patently ridiculous. Any thought of reprisals or blacklists is ridiculous."

Hansen also complained, as did NCAA President J. Neils Thompson in a letter to the subcommittee, that the NCAA was being treated unfairly since only one side - the anti-NCAA - has been heard so far.

The battle between the NCAA and Minnesota began when the university's basketball program was placed on two-year probation in 1976. The NCAA also ordered the university to suspend three players - All-American Mychal Thompson, David Winey and Phil Saunders.

An internal university group investigated the charges and balked at placing the three on probation. The NCAA then put the entire men's athletic program on probation and threatened to cancel all postseason competition for Big Ten colleges, which came to the support of conference member Minnesota.

The internal investigation was necessary to provide athletes with due process as required under state law and as part of the university's obligation to "self-police," Magrath said.

An NCAA official told him, Magrath said, to conduct whatever investigations the university thought it had to, but to reach the right decision.

After Minnesota losts its appeal to the NCAA, the university's internal committee agreed to place the three on probation, although a court order precipitated a suspension of only the first nine games this season. The men's basketball team is the only one currently barred from postseason competition.

"I confess we did eventually sacrifice principle for expediency," Magrath said.

Magrath said he does not favor federal control of college sports, but suggested that if the NCAA does not reform itself, then Congress must intervene and mandate changes.

Noting that membership in the NCAA is about as free-will and spontaneous as paying one's tazes, Magrath said the organization has an "unchallenged system of rewards and punishments . . . (enabling it) to regulate the intercollegiate athletic market with the immunity of a protected monopoly."

The distribution of television income and exposure is one such mechanism, he said, because of its effects on recruiting and balancing the budget.