Donald Kagan had been in prison for murder for more than a decade when doubts about his guilt arose from an uncommon source: the former judge who had convicted him.

The reason was more extraordinary still: The now-retired, white jurist felt he had been swayed by bias against Kagan, also white, in the killing of a black man.

On Wednesday, another judge upheld the conviction in the 1998 case. Acting Brooklyn state Supreme Court Justice ShawnDya Simpson said she found the case emotionally wrenching but that legally, there were no grounds to reverse the conviction.

"It's unfortunate that my hands were tied" by the law, Simpson said. "This may be one of those cases that bothers me for the rest of my life."

Kagan sat still, looking downward, after hearing her decision. His lawyers said they would appeal.

Kagan, 40, has always maintained he was defending himself in a confrontation with Wavell Wint outside a Brooklyn movie theater in November 1998. Kagan said Wint had grabbed the gold chain he was wearing; Kagan shot him with a gun he said he had flashed at Wint earlier to ward him off. Wint was unarmed.

Then-state Supreme Court Justice Frank Barbaro heard the case without a jury, convicted Kagan in 1999 and sentenced him to 15 years to life in prison. An appeals court upheld the conviction, saying there was evidence that Kagan escalated a scuffle that stemmed from an argument, not a robbery attempt.

"We are satisfied that the verdict of guilt was not against the weight of the evidence," state Supreme Court Appellate Division judges wrote in 2004.

But Barbaro, as time passed, wasn't so satisfied. A former longshoreman and labor lawyer, onetime mayoral and congressional candidate and 24-year state assemblyman, the Democrat had retired from the bench in 2003 after six years as a judge.

As he read news accounts about wrongful convictions, he started to question his verdict in Kagan's case. Re-reading the transcript, the longtime civil rights advocate became convinced he had done an injustice: His own hatred of anti-black racism had tainted his view of the conflict between Kagan and Wint, leading him to believe Kagan acted out of bigotry and misinterpret facts that supported his self-defense argument, the former judge said.

"I saw a black man being killed by a white man, and that triggered my unconscious in ways I wasn't aware of," Barbaro said Wednesday by phone from his home near Albany.

Although he was convinced at the time of the trial that he conducted it justly, "when I came to the conclusion that I had made a mistake, I've been tortured by this ever since," said Barbaro, who contacted Kagan's lawyer, who asked a court in 2011 to overturn the conviction.

Barbaro said he was "outraged" by Simpson's decision and hoped Kagan's planned appeal succeeded.

"The man was not given a fair trial. Those facts are irrefutable," he said.

The Brooklyn district attorney's office argued the conviction should stand.

Kagan has applauded Barbaro for coming forward with his misgivings. "Not many people would do that, especially after all this time," Kagan told the Post in a jail interview in December.

But Wint's relatives expressed anguish at revisiting the case.

"I thought everything was over with," his son, Wavell Wint Jr., told the Post in December.

"It was a little nerve-wracking, but I'm satisfied with the decision," Wint's sister-in-law, Lisa DeJesus, said Wednesday. "She made the right decision. Why overturn something now?"