The Harvard Law School has offered a position to the Philippines' most prominent political prisoner, thus embroiling itself in an election here which could have a major impact on the future of U.S. relations with its former colony.

Philippine President Ferdinand Marcos is known to have expressed annoyance at suggestions by the U.S. Embassy here that he free former senator Benigno "Ninoy" Aquino, Jr., to accept a post as visiting scholar at Harvard. Marcos added the offer to a long list of grievances - including a dressing down he received from President Carter's top human rights aide - in a nationwide television broadcast Wednesday night at the close of the first election campaign here in six years.

After 30 years as the favorite target of Philippine parties out of power, the alleged arrogance of the U. S. government has been grasped by Marcos as his own issue to win nationalist support for his martial law administration. Yet he has shown little sign of wanting to reduce ties with the United States and he seems to have timed today's election for an interminational Assembly in large part to soothe U.S. critics who might block an upcoming military bases agreement.

Harvard's East Asian legal studies program asked Aquino, now confined to a room at an army fort here, in November to become a visiting scholar. The offer was not disclosed at the time. Aquino heads a slate of anti-Marcos candiates seeking Assembly seats in today's election. He was jailed on charges of subversion, murder and illegal arms possession the day martial law was declared in September 1972, when he was one of Marcos' sharpest critics and a favorite for the presidency in 1973.

"We think he would have much to tell us about due process in the Phillipipnes ," said law professor Jerome A. Cohen, director of the Harvard program, in a telephone interview. Cohen was also instrumental in a so far unsuccessful invitation to South Korean political prisoner Kim Dae Jung to speak at Harvard. Cohen said he has also invited supporters of the Philippine, and South Korean governments.

Cohen said he first cabled Marcos asking that Aquino be freed to go to Harvard in 1975. He said Marcos has never replied to any of his letters or cables.

Aquino's wife, Cory, said Marcos did not tell her husband of the 1975 offer, but did pass on the more recent offer to Aquino. Prison authorities made the unusual gesture of allowing Aquino to telephone her to discuss it.

"Naturally we were very elated," she said. But Marcos has given no indication lately he plans to free Aquino, 45. Also, it is uncertain if the former boy wonder of Philippine politics would accept what would be, in effect, exile and an end to any real hopes of future high office here.

His presence in jail has contributed to tensions between Manila and Washington. Several members of the U.S. Congress have appealed to Marcos for Aquino's release. When a military death sentence - now temporarily withdrawn - was announce for Aquino Nov. 25, a U.S. State Department spokeswoman expressed official concern.

Marcos is in the midst of renegotiating treaty for American use of the huge Clark Air Base and Subic Naval Base. When signed, the new treaty is expected to double compensation for use of the bases from $100 million to $200 million a year. The need for congressional approval of that treaty is thought to have strongly influenced Marcos' decision to call the Assembly election now and let Aquino participate.

Future relations with Washington may hinge on whether Marcos tampers with the ballot counting today so that a pro-Marcos slate can have a clean sweep, or gives Aquino and his supporters a chance to win some seats.

Despite daily headlines in the Marcos-guided newspapers warning of foreign interference in the elections, it is unclear how much the issue actually concerns Filipinos. They clearly resent what they regard as mistreatment by rude American tourists, and they often hear stories of discrimination from friends and relatives in the United States.

But, there is near universal approval for the democratic tradition and the culture and technology brought to the islands during 50 years of American colonial rule.

"I am glad it was the United Staes that came to us," Marcos' wife, Imelda, who heads the pro-Marcos Assembly slate, once said.

The visit of Patricia Derian, U. S. assistant secretary of state for human rights, in January still rankles Philippine government officials. The often outspoken Derian "began to lecture us on how our opposition parties should be treated and how our court trials should be conducted," Marcos said on television.

He also accused "foreign" interests of funding a program of cash grants to samll shopkeepers in Manila slums being given out by Trinidad Herrera, a leftist organizer on the anti-Marcos ticket, who was freed from detention last year after a Carter administration protest. Herrera said yesterday the money came from several donors, including American-backed church groups.

Marcos has been concerned enough about his U.S. image to hire a New York public relations firm and have the foundation that holds most of his personal assets set up a special program on Philippine studies at the Fletcher School in Massachusetts.

"Perhaps we could also get Fletcher to make Aquino a visiting professor," Harvard's Cohen suggested.