Bacani, one of the Philippines’ most popular Roman Catholic bishops, apologized and offered to resign from his post as head of the church’s Novaliches diocese.
In a statement apologizing to priests, followers and his secretary, Bacani denied the accusations but acknowledged making an "inappropriate expression of affection."
Monsignor Romulo Ranada, Bacani’s spokesman, said Bacani will be in the United States to visit his mother and other relatives as well as receive medical treatment.
Ranada insisted that Bacani was not trying to evade reporters.
The Vatican, which appoints Philippine bishops to local dioceses, has begun "a full-blown investigation" into the allegation and may make its decision in three weeks, Ranada said.
Church authorities "took it seriously" because it was not an "anonymous complaint," he said.
In a statement issued shortly before his departure for the US, Bacani said he was "deeply sorry for the consequences of any inappropriate expression of affection to my secretary."
"I have deliberately kept silent to you about this matter and its aftermath because I did not want to cause you any undue anxiety," he said.
Without referring directly to the alleged incident in March, Bacani said he had "put myself in the hands of the Church, ready to leave the diocese if necessary for her good, and I am now taking ample time for rest and prayer in solitude."
He said he has relayed to the papal nuncio, Pope John Paul II’s representative in the Philippines, his side of the matter.
"I beg the Lord again for mercy. I also ask pardon of Mother Church and of all of you and my secretary who felt hurt," Bacani said.
Earlier, in a radio interview late Saturday, Bacani asked the public to be skeptical of the charges, advising them to "be careful or they could be tricked. Don’t believe in intrigues."
Ranada said while Bacani may have expressed affection inappropriately, there was no malice in his actions and denied the gestures constituted sexual harassment.
"They were shocked, everybody was shocked and I myself cried. Many of us were hurt, but that was our gut reaction, nothing has been proven," Ranada told The Associated Press by telephone.
But there was no mention of the scandal in yesterday’s homilies. "I don’t think there was a need for it to be mentioned," one priest told The STAR after celebrating a Mass.
One churchgoer said the "altar is not really the place where it should be settled."
"If it should be discussed, there should be a special meeting of that among parishioners," he said. "If I heard about that in the homily I would be distracted because I went to Mass for a more important reason."
Ranada raised the possibility that the scandal was being played up by rival religious groups that were trying to discredit the Catholic church.
"The clergy and the lay leaders are fully behind the bishop," he added.
Bacani’s deputy, Monsignor Gerardo Tapiador, said while priests at the Novaliches diocese were bothered by the accusation, the "entire clergy is solidly behind the bishop. We stand behind him."
Ranada also denied reported attempts by Church officials to keep a lid on the scandal.
Marites Vitug, editor-in-chief of the fortnightly magazine Newsbreak, which broke the story last week, earlier told The STAR in a telephone interview that copies of the magazine were "bought by the hundreds by priests."
Church personnel waited at their Mandaluyong City office to buy copies before they hit the newsstands, she said.
"I don’t think we can buy all of the magazines. There is no such effort. We cannot keep on buying. The magazine can just print more," Ranada said.
Newsbreak reported that the secretary, in her mid-30s, recently complained to church officials and a left-wing women’s group, Gabriela.
Bacani allegedly made sexual advances to her twice, most recently in March when he tried to hug her. She resigned shortly.
Bacani, 63, is known for his ready smile and charisma, especially among the poor.
He was among the most vocal Church leaders who actively opposed the late dictator Ferdinand Marcos in the 1980s and later helped draft the 1987 Constitution.
Known for his advocacy of the poor, he is considered an activist in a Church considered a bastion of conservatism.
Bacani has gained national attention as a critic of public utilities and of government policies, using a regular newspaper column as his pulpit.
He has also served as a spiritual adviser of the politically influential El Shaddai, a Catholic religious group with thousands of adherents in the Philippines and which reportedly raises huge amounts of money from contributions.
El Shaddai said it would determine the facts and hear Bacani’s side before making any comment on the scandal.
Bacani, along with El Shaddai leader Mike Velarde, is also the spiritual adviser of detained former President Joseph Estrada, Mrs. Arroyo’s political nemesis who is now facing a corruption trial.
Bacani’s association with Estrada did not sit well with the Church leadership, which was critical of Estrada because of his image as a womanizing drunk who gambled a lot.
Philippine Church officials had no immediate reaction. A Church source said Manila Archbishop Jaime Cardinal Sin, the Church leader in the country, was deeply saddened.
Church officials here traditionally have avoided publicly discussing sexual offenses by priests, who usually are among the most revered and influential community leaders in this predominantly Roman Catholic nation, particularly in rural areas.
In recent years, the Roman Catholic Church worldwide has been hit with sexual scandals in countries including Australia, Austria, Britain, Canada, France, Germany, Ireland, Mexico, Poland and the United States.
Early last year, the Catholic Church in the United States was rocked by scandals involving American clergymen who allegedly sexually abused boys serving in church.
Aghast by the gravity of the scandals, Pope John Paul II strongly denounced sexual misconduct by clergymen as a "crime." Later, the spotlight on priests exposed similar allegations involving Filipino clergymen in the Philippines.
In July, the CBCP apologized for what it said were grave cases of sexual misconduct by Filipino priests in recent years and vowed to prosecute and defrock offending clergymen.
It added it has drafted guidelines to address various types of sexual abuse and misconduct by priests.
The Catholic church claims more than 80 percent of Filipinos as followers and church leaders often criticize public policies on matters like population control, human rights and national security. — With Nikko Dizon, AP, AFP