Oscar Cruz, a retired archbishop overseeing the investigation, told Al Jazeera's 101 East programme that in recent years more cases had come to the church's attention.
"Yes, yes, yes... [there are] more reports on paedophilia and homosexuality," Cruz said. "It is a heinous crime, you know. And a priest at that? Violating a minor? Come on!"
"If clerical abuse victims take on the most powerful institution in the Philippines, it is a David and Goliath battle," 101 East's Drew Ambrose, reporting from the capital Manila, said.
In an interview with Al Jazeera, "Imelda" said she was sexually assaulted by a priest three years ago, when she was 15.
After she filed a police report, two members from her village church paid her $150 to drop the case, she alleged.
"At first, I didn’t really want to accept the money because I already knew it was from a priest, but they were so insistent that I take the money," she said.
Jaime Achacoso, a lawyer and expert on the Catholic Church's canon law, said priests found guilty of sexual misconduct had not been removed from ministry.
"Oh yes, they weren’t, unfortunately. And the inadequate investigations in the past have festered, so things have not been solved," he told Al Jazeera. "Priests continue to be there."
'Scale of abuse' unknownMerian Aldea, an outreach worker helping victims of abuse, said some of them had barely started school and were often terrified to speak out.
"The youngest is six. They are afraid they will be cursed or 'God' will curse them if they go against these people."
Observers say that is just one reason why the full scale of abuse by Filipino priests may never be known.
The Vatican and the Archbishops of Manila and Cebu refused to comment on the investigation.
Among the most high-profile accusations of abuse was one from Philippine President Rodrigo Duterte, who has repeatedly said the church hierarchy are "hypocrites".
Duterte said that, during his teenage years, he and other male classmates were molested by an American priest while attending a Jesuit school in his hometown of Davao.
"This religion is not so sacred," he was quoted as saying.
He also said he was too young and frightened to file a complaint against the priest, who was later linked to similar abuse after he returned to the United States.
You can watch the full 101 East film, Philippines: Sins of the Father, on aljazeera.com at any time after that.