Meanwhile, the Catholic Bishops Conference of the Philippines (CBCP) broke its silence on the scandal, urging its flock to remain steadfast in the faith and saying the Church does not revolve around its clergymen.
Mrs. Arroyo said she was confident the Roman Catholic Church which has come under public scrutiny on how it would react to the latest sex scandal to rock the faith would overcome the crisis.
The government will not interfere unless it is clear that a crime has been committed, Mrs. Arroyo said, adding that "both sides have a right to be heard and the right to impartial justice."
"I am saddened by the turn of events, but I also know that the Church has the leadership, fortitude and strength to surmount these trials," Mrs. Arroyo said in a statement read by her spokesman, Ignacio Bunye.
"The government shall not involve itself in this issue unless there is culpable violation of law," the President said. No criminal case has been filed against Bacani.
Mrs. Arroyo co-authored the law against sexual harassment when she was a senator, before she was elected vice president in 1998. The Constitution forbids government interference in the affairs of churches and religious organizations.
"Let us avoid prejudgement," Mrs. Arroyo said. "This is a time for sobriety, fairness and prayer. Let us not dwell on speculations and rumor. The least we can do is to pray and hope that this crisis will be over soonest."
Bishop Orlando Quevedo, CBCP president, admitted that the case, as well as others that have recently buffeted the influential Church in the country, "reinforces the negative opinion of cynics, skeptics and critics regarding the Church."
He reminded the faithful that the Church does not center on any person.
"The reason we love the Church and the reason we believe the Church is not due to the personality, the charisma, or the intelligence of this or that priest or bishop. We love the Church and believe the Church because the Church comes from Christ," Quevedo said in a statement.
He said the "sad situation may also shake the faith of not a few."
"In all this, the Church must remain credible and courageous as a moral authority in the face of the moral implications of the many social, economic and political problems in our country," Quevedo said. "Even when besieged, the Church cannot remain silent about other problems."
The Catholic Church in the Philippines has been largely silent on priestly misconduct in the past but a sex abuse scandal in the United States last year brought the issue to the fore.
Aghast by the gravity of the scandals, Pope John Paul II strongly denounced sexual misconduct by clergymen as a "crime."
In an unprecedented move, the CBCP in July last year publicly apologized for sexual abuses committed by Filipino priests, but insisted that a majority of clergymen remained faithful to their vows.
The Church also admitted that some 200 priests were investigated for sexual misconduct over the past 20 years, some of whom were dismissed while most resigned voluntarily.
Church officials have since admitted around 1.6 percent of the local clergy have been sexually active. Men planning to be priests swear a vow of celibacy before they are ordained.
The Philippines is Asias largest Roman Catholic country with about 85 percent of the 82 million people following the faith. Most of the countrys Muslim minority are concentrated in the south, in Mindanao.
A devout Catholic, Mrs. Arroyo had the backing of the Catholic Church during the January 2001 popular uprising that deposed President Joseph Estrada, her predecessor and political nemesis.
Mrs. Arroyo, then the vice president, replaced Estrada who is on trial for allegedly running an illegal gambling protection racket, among other corruption charges, during his 31-month presidency.
Bacanis becoming a spiritual adviser of Estrada did not sit well with the Church leadership, which was critical of Estrada because of his image as a gambler, a womanizer and a drunk.
Yesterday, Mrs. Arroyos adviser on ecclesiastical and media affairs, Conrado Limcaoco, visited the Manila office of the CBCP, the countrys largest association of Catholic bishops.
He denied speculation that he delivered a sympathy letter from Mrs. Arroyo. "No comment. The less said on this issue, the better. Lets give dignity to the people concerned in this matter," he said.
As Mrs. Arroyos point man with religious organizations, Limcaoco said he regularly visits the CBCP office.
Sen. Robert Barbers, a friend of the bishop, declined to comment but said Bacani "should be given his day in court."
"Its not really good for me to say anything about the scandal involving Bishop Bacani because he is our family friend. Some people might say that we are supporting him," he told reporters. With Jose Aravilla, Jose Rodel Clapano