NEW YORK, United States (CMC) — A Jamaican-born pastor charged with raping a 12-year-old female member of his congregation has turned down a plea deal that included a three-year prison term.

Michael Clare, 38, refused the offer from prosecutors, despite "almost irrefutable proof" he impregnated the child, said Bronx Supreme Court judge Megan Tallmer.

"He wasn't interested," Tallmer said in court Monday.

But Clare's lawyer, Paul Brenner, asked the judge to consider probation instead of prison.

"I would never do that," she snapped, citing a DNA match between Clare and the victim's aborted foetus.

Clare, the married leader of the Harvest Worship Centre in the Bronx and principal of the Associated Harvest Prep school, declined comment outside court.

Authorities learned of the alleged crimes in June, when the girl, now 15, told her parents and police that Clare had been having sex with her for three years.

Clare, who is free on US$50,000 bond, faces up to 25 years in prison if convicted of first-degree rape at trial.

Prosecutors alleged that he may have victimised other young churchgoers as well.

The judge said his preaching days are probably over, though, since his name would likely be added to the state sex offender registry following any plea deal.

"I don't see how he could continue his work as a pastor," Tallmer said.

Clare's lawyer said the clergyman will be vindicated at trial.

"He turned down the plea deal because he's innocent," Brenner said.

But one prosecutor said that was a mistake.

"This was a sweetheart offer considering the evidence against him," the prosecutor said. "It won't get any better from here."