The NYPD missed the chance to pursue accused child molester Steven Pappas two years ago because they didn’t believe the story told by a 12-year-old victim who came forward back then, Police Commissioner Ray Kelly revealed today.

“What happened is when he spoke to the Special Victims Unit when this happened in 2009, they weren’t certain of his credibility,” said Kelly, following an interfaith breakfast in Midtown.

“His mother sees this individual who was arrested — Pappas’ picture — on television, finds out the circumstances were very similar to what her son reported. She calls the (police) hotline and that’s how we got involved to investigate.”

Pappas, 50, was arrested Thursday after a 15-year-old told police Pappas approached him at the 53rd Street subway station in Sunset Park, Brooklyn, pretended he was a cop and drove him to 92nd Street in Bay Ridge, where he was sexually assaulted.

Kelly said the 12-year-old told a nearly identical story of being approached at the same 53rd Street station by someone posing as a cop who drove him to a parking lot, where he was attacked.

It is the second bombshell in the heinous case.

Kelly had earlier disclosed that Pappas was carrying the badge of an active duty police officer. Today, he reported he was actually carrying a duplicate badge that someone he knows gave him this month.

Although it missed the opportunity to get Pappas off the streets two years ago, Kelly defended the Specail Victims Unit.

“You have to judge credibility. It’s a very sensitive area. the special people are trained in this, do it extremely well and in this instance it proves the young man– the boy– was correct,” he said.

“But that’s what happens in this business. There’s a fair amount of recantation that takes place as far as the claims of sexual abuse. It’s a sensitive, complex area. I think they do it well. I think the important thing is that this individual is under arrest.”