BOSTON — The archdiocese accepted the resignation of Father Walter Cuenin as pastor of Our Lady Help of Christians in Newton after financial irregularities were discovered in a parish audit, the Archdiocese of Boston said in a Sept. 26 release.

According to the archdiocese, Father Cuenin improperly accepted stipends from the parish in excess of archdiocesan policies, drove a car leased by the parish, and accepted compensation from both the parish and the archdiocese while on a sabbatical.

Father Christopher Coyne was appointed to replace him as pastor of Our Lady’s Sept. 27.

The improprieties were first discovered “during a routine annual payroll audit of 20 parishes that included Our Lady Help of Christians in Newton,” the archdiocese said in the statement issued in response to the outcry over the popular priest’s resignation.

“As a result, the Archdiocese commissioned DeLoitte & Touche to conduct a comprehensive audit at Our Lady’s in order to gain more information about the non-conforming practices that were uncovered and the overall state of parish finances,” the statement continued.

The archdiocese said Father Cuenin has agreed to reimburse the parish between $75,000 and $85,000.

Father Cuenin had recently completed his second 6-year term as pastor of Our Lady Help of Christians. According to archdiocesan spokesman Terry Donilon, Father Cuenin will likely be reassigned.

In a letter to parishioners announcing his resignation as pastor, Father Cuenin said that the archbishop has suggested he “become more involved in ecumenical and interfaith relations.”

Father Cuenin defended his actions on the stipend amounts, saying that the practice was already in place when he arrived in 1993. He also admitted to the use of a parish-leased car, although he said it was authorized by the parish finance council.

Members of Our Lady’s finance council issued their own statement saying they had approved Father Cuenin’s expenditures and were unaware they were in violation of Church rules. The church’s previous pastor had received similar benefits without objection from the archdiocese, they said.

In response, the archdiocese stated that the rules about stipends and expense reimbursements are regularly updated and circulated to all clergy.

“Father Cuenin’s resignation was requested in accordance with archdiocesan policy, which is consistently applied throughout the archdiocese.”

Although in his letter Father Cuenin asked his parishioners not to protest his removal, some parishioners held an overnight prayer vigil Sept. 26, dismissing the archdiocese’s reasons for removing Father Cuenin and claiming he was targeted because of his history of speaking out. 

Father Cuenin was a critic of former Archbishop Cardinal Bernard Law’s handling of the clergy sex abuse crisis and was one of 58 Boston-area priests who signed a letter in 2002 calling for Law’s resignation.

He has also questioned some Church teachings on gays and the ordination of women. Between December 2002 and September 2003, the archdiocese banned archdiocesan gatherings at his church after Father Cuenin aired some of those views in The New Yorker Magazine.

Approximately 400 people attended the start of the all-night vigil.

Father Cuenin declined to criticize the archdiocese during interviews after a pre-arranged talk in Dedham on Sept. 26. But he said the archdiocese never objected to his compensation during several previous audits of the parish.

“I feel sad to leave Newton,” Cuenin said. “I understand the people’s sorrow and loss, but I hope they welcome their new pastor.”

Our Lady’s new pastor, Father Coyne said he understood the concerns of parishioners.

“I’m going to the parish very excited, but also very apprehensive, because I know people are upset,” he said.