A nun who is accused of stealing $128,000 from two Orleans County churches spent more than nine months last year at a treatment facility for gambling addicts, a leader of her religious order said Monday.

Sister Mary Anne Rapp has “maintained her recovery” since completing her treatment earlier this year, said Sister Edith Wyss, provincial minister for the Sisters of St. Francis of Penance and Christian Charity.

In the first local case of its kind involving a nun, Sister Mary Anne, 67, a Lewiston resident, was arraigned Monday night on charges that she stole from two churches where she worked in the Town of Kendall and the Village of Holley.

Her Buffalo attorney, James P. Harrington, entered a plea of not guilty on behalf of Sister Mary Anne to a single count of second-degree grand larceny, a Class C felony, before Justice Craig D. Lape in Kendall Town Court.

According to Orleans County District Attorney Joseph V. Cardone, the nun is accused of embezzling from St. Mark Church in Kendall and its sister church, St. Mary, in nearby Holley. The thefts took place between March 2006 and April 2011, according to the Orleans County Sheriff’s Office.

“She was very quiet and very cooperative,” Cardone said after her court appearance. “She was greeted by a number of parishioners who were there to support her.”

Harrington agreed to waive the case out of Kendall Town Court, Cardone said, and Sister Mary Anne was released without bail. The case will go before a grand jury, Cardone noted, unless an agreement on a plea and restitution can be worked out within 45 days.

Sister Mary Anne stole money donated by church members because she was frequently gambling at casinos, mainly the state-operated casino at the Batavia Downs horse racing track, a source familiar with the case told The Buffalo News.

After an audit of church finances was conducted by the Catholic Diocese of Buffalo, Sister Mary Anne was placed on administrative leave in February 2011, removed from duty at the two churches and sent for treatment for her “gambling addiction,” said her superior, Sister Edith.

“When she was placed on administrative leave from her parishes, … she agreed at our order’s behest to seek treatment for her gambling addiction,” Sister Edith said. “She spent 9½ months in an inpatient treatment program and has maintained her recovery … since. As sisters, we continue to pray for Sister Mary Anne and help her deal with her addiction, which is sadly prevalent in our society.”

Sister Mary Anne is one of 138 members of the Sisters of St. Francis of Penance and Christian Charity, which is based at the Stella Niagara motherhouse in Lewiston.

“This is a very difficult time for all of us, especially those of us who have lived and worked with Sister Mary Anne for her nearly 50 years in our community,” Sister Edith said in a statement sent to the news media. “We cannot and do not condone the conduct alleged in these charges. … The investigation and the legal process must run their course, and we have no further comment at this time.”

The case was handled by Investigator Corey Black of the Orleans County Sheriff’s Office, who received information from auditors of the Buffalo Diocese and other church officials.