Priest Takes Leave After Youths’ Sex Allegations : Homeless: The founder of Covenant House denies all charges leveled by three former residents of the refuge for runaways.

Father Bruce Ritter, the widely praised Franciscan priest who founded the nation’s largest system of shelters for runaway teen-agers, on Tuesday was removed temporarily as head of Covenant House amd new reports that he sexually abused some of the troubled youths his organization sought to help.

The Franciscan Order is investigating the allegations and has directed Ritter “to begin a period of rest and recuperation without responsibility for Covenant House until this inquiry is completed,” Father Conall McHugh said in a statement.

On Tuesday, the New York Times reported that a former Covenant House resident claimed to have been drawn into a sexual relationship with Ritter in 1973, after the client had turned to the program for refuge from the streets. It was the third such accusation to have been leveled against the 62-year-old Roman Catholic priest since early December.

The first charges prompted Manhattan Dist. Atty. Robert M. Morgenthau to open a criminal investigation, which continues.

Ritter again denied all the allegations and issued a statement saying he will “take several weeks off to rest and recuperate to deal with the personal stress caused by this controversy as well as its impact on Covenant House.”

Covenant House’s board of directors held an emergency meeting Tuesday night. “I don’t believe the charges,” insisted board member Ellen Levine, editor in chief of Woman’s Day magazine. Levine said Covenant House had expected “copycat” allegations from embittered former clients after the initial reports reached the news media.

The first allegations were levelled against Ritter in December by Kevin Kite, a former prostitute who told the New York Post that the priest had lavished gifts and money on him in exchange for sex last year while Kite was part of the Covenant House program.

Kite’s father, Alton Kite, subsequently denounced his 26-year-old son as a habitual liar.

On Jan. 24, the Village Voice reported that another former Covenant House client, John P. Melican, also claimed to have had a sexual relationship with Ritter that spanned 13 years.

The third accuser, Darryl J. Basile of Ithaca, N.Y., said he was sexually involved with Ritter in 1973, when he was 14 years old.

“I am profoundly saddened by the allegations against me and the need to deny them constantly,” Ritter said in a statement issued by Covenant House. “I devoutly hope the inquiries under way will bring an end to this incredibly painful chapter in my life.”

The scandal has devastated the organization, which raised $87 million in 1989 and claims to help more than 25,000 runaways a year. Much of its success has hinged on the personal charisma of Ritter, who was hailed as a hero in former President Ronald Reagan’s 1984 State of the Union address. It was only one of many accolades he has collected over the years.

Covenant House dwarfs all other efforts to reach runaways, including the federal government’s. “There’s nobody else out there taking care of the young people,” Levine said.

One of Covenant House’s most recent expansions was a controversial move last year into Los Angeles. Other Los Angeles organizations protested that Covenant House, with its national reputation and fund-raising muscle, would put them out of business. As a result, Covenant House scaled back its plans for a 100-bed shelter and opened one with only 20 beds on Hollywood Boulevard.