NEW YORK (AP) _ Covenant House officials thwarted investigations into the murder of a young man who appeared prominently in the shelter's publications, New York Newsday reported today.

Covenant House, the largest shelter organization for runaways, denied knowing the victim, Sean Russell, 23, when a private investigator inquired about his murder last year, Newsday said.

Months later, acting Covenant House president Frank Macchiarola discovered internal memos discussing a possible cover-up, he told Newsday. The memos contained allegations Russell was involved with a drug and prostitution ring operating from shelter facilities, he said.

Macchiarola had been named last month to replace the Rev. Bruce Ritter, Covenant House's founder, who resigned after allegations of sexual misconduct with young runaways. Covenant House is the world's largest network of shelters for teen-agers.

Macchiarola resigned after the trustees of the charity obstructed his attempts to investigate Russell's death, he told Newsday.

Officials of the embattled charity declined to comment Monday, Newsday said.

According to an account pieced together by Newsday, Russell had become romantically involved with a 27-year-old woman. On Oct. 20, her ex-lover, Donald Holden, 45, tied up and raped the woman, fatally stabbed Russell and then committed suicide by slashing his own throat.

Russell appears on page one of the organization's annual report for 1989, and is featured in the charity's official calendar, which is received by thousands of contributors.

According to Newsday, shelter officials deceived a private investigator, Michael Lipowski, dispatched to look into Russell's death.

Lipowski told Newsday that a lawyer for Covenant House and one of its counselors, Paul Bates, flatly denied that Russell had any association with the organization.

Bates acknowledged Monday that he was Russell's counselor but refused to discuss the young man's life or death, Newsday said.