A 1971 probe into alleged misuse of American aid funds by a Jesuit priest in Chile was shelved to avoid embarrassing Washington's Chilean political allies, according to the National Catholic Reporter.

In an article scheduled for publication today, the unofficial weekly newspaper dealing with Catholic affairs says the investigation involved a Bedgian missionary, teh Rev. Roger Vekemans. He was a key adviser during the 1960s to Chile's Christian Democratic president, Eduardo Frei.

Vekemans has been mentioned frequently in connection with charges that he acted as a conduit for Central Intelligence Agency funds intended to support anti-Communist political forces in Chile. Vekemans, who has denied these charges, left Chile after Salvador Allende, a Marxist, was elected to succeed Frei in 1970.

The NCR article by an American writer, Richard L. Rashke, is based on U.S. government documents obtained under the Freedom of Information Act. It says the Agency criminal investigation of Vekemans after an audit showed apparent irregularities in the use of $400,000 given the priest by AID to study Latin American population problems.

According to Rashke's article, the audit showed that Vekemans had billed AID for services not received, costs not incurred and extraordinary bonuses, wages, transportation and entertainment costs that violated the terms of the AID grant.

However, the article continues, the investigation was dropped after the then U.S. ambassador in Chile, Edward Korry, protested "that a criminal action against Father Vekemans would specificially contradict U.S. objectives in Chile."

The article quotes Korry as advising Washington "that Father Vekemans was very closely associated with the Christian Democratic Party, the Roman Church and with other forces that were anti-Communist . . ."

"I would conclude that an effort to mark him as a criminal would serve primarily those forces dedicated to defaming the Christian Democratic government of Frei and its successors," Korry said.

The ambassador did recommend that U.S. officials attempt to get Vekemans to repay the disputed funds. However, according to the NCR articles, AID records contain no sign that Vekemans repaid any of the money.

Rashke's article also retraces several proviously published stories about Vekemans and his alleged dealings with the CIA, including the assertion of an American priest, the Rev. James Vizzard, that Vekemans told him of receiving $5 million in secret CIA funds and another $5 million in regular U.S. foreign and after a 1963 meeting with President Kennedy.

The article says that Vekemans, who now lives in Bogota, Colombia, refused to be interviewed by Rashke or to comment on any of the allegations.