After almost two years of study, the President's Commission on Olympic Sports will recommend "fundamental changes" in the U.S. Olympic Committee as part of a comprehensive overhaul of the amateur sports systme in this country.

Michael T. Harrigan, executive director of the commission, declined to give specifics on the USOC proposals. The commission's report will be unveiled Thursday in New York.

But Harrigan agreed to talk about the general thrust of the report in an interview during which he outlined the various issues and problems the commission dealt with in trying to reform U.S. amateur sports.

Besides changing the structure of the USOC, the commission also is recommending legislation on matters such as resolving disputes among the country's many amateur sports groups, most notably the Amateur Athletic Union and the National Collegiate Athletic Association.

There are also sections on athlete's rights d, designed to protect the athlete from being penalized by one organization for participating in an event sponsored by another, financing amateur athletics, developing world class athletes and sports medicine.

The report also covers the roles of the military, women and the handicapped in sports with specific proposals one enhancing involvement by those groups.

On the issue of amateurism, there will be suggestions for changing the various definitions that have caused some athletes to be declared imeligible in domestic sports.

"We've all heard complaints that America is sending amateurs to compete against other countries' professionals," said Harrigan. "We have found that some of our national governing bodies have stricter rules on amateurism than they are required to under international rules."

Congressional legislation will be required for many of the commission's proposals, such as the restructuring of the USOC, a congressionally chartered but essentially a private corporation.

Citing the need for an overhaul of the national governing bodies, Harrigan said, "The power blocs which have crippled the organization of amateur sports for such a long time will be eliminated."

He added that there will be a system "of checks and balances so various groups can gain appropriate and fair representation in national governing bodies."

To assure this, he said, there will be financial penalties for noncompliance and there will be financial incentives in another, unspecified way.

The report also deals with various measures for funding amateur sports from the private and public sectors. There are suggestions for commemorative coin sales, lotteries in states that have them and an excise tax on professional sports that use the amateur groups, including colleges, as "farm teams" for their sport.

The report also examines the sports systems of other nations. Despite governmental denials, many of these sports organizations are run by governments in violation of the rules of the International Olympic Committee.

Because the IOC forbids governmental intervention, the USOC, after the proposed reorganization, will still be autonomous but, in some cases, it will be accountable to the government, by periodical progress reports, particularly if there is federal aid involved.

In the "overview" section of the report, which was made public, the commission said: "The men and women who administer the various sports organizations are almost invariably sincere and self-sacrificing and have only the best interests of their sport at heart. Both they and the athletes are victims of a gawky, uncoordinated collection of programs unworthy of being called a system."