Officer William Cozzi was on-duty when the beating occurred.
On Thursday, Cozzi was sentenced to more than three years in prison.
The officer had earlier pleaded guilty to a state misdemeanor charge and sentenced to 18 months probation. But in a move that angered many other officers, Police Superintendent Jody Weis referred the case to the federal government.
And Cozzi's lawyer says that wasn't right.
"The prosecution brought by Supt. Weis was misguided and vindictive," said Terry Gillespie, Cozzi attorney.
Officer William Cozzi had an unblemished record during his 15 years on the force. Until August, 2005, when his lawyers say he simply snapped.
It happened at Norwegian American Hospital. Randall Miles, 60, was there to be treated for a stab wound. He was drunk and belligerent so the hospital called police.
Even though Miles was shackled to a wheelchair, prosecutors say a surveillance video shows Cozzi hit him about 10 times with a police club called a sap.
Cozzi pled guilty in state court, was sentenced to probation and was suspended from the force for two years.
As he was about to return to work, Superintendent Jody Weis referred the case to federal prosecutors who charged Cozzi with violating Miles' civil rights.
Cozzi pled guilty. He admitted his mistake and apologized. But Judge Blanche Manning called his actions deeply troubling and sentenced him to three years and four months in jail. And Cozzi loses his pension.
Other cases involving police officers - worse facts, worse records - are routinely brought down to misdemeanors and pensions are saved. What makes this case so different other than the videotape.
But Cozzi damaged his position further by falsifying the records of the case.
"Police officers and the public need to understand that when people cross the line and assault someone and then lie about it, that has to be addressed, too. It may not be popular, but we have to do that," said Pat Fitzgerald, U.S. Attorney.
The Fraternal Order of Police says the case has seriously damaged relations between Weis and the rank and file.
"I think the greater part of it is a misunderstanding by the superintendent as to what real justice is here," said Mark Donohue, Fraternal Order of Police.
"I got a message for all those fine officers in blue. After 15 years don't snap or you'll be thrown under a bus, a federal bus, by your own superintendent," said Gillespie.
Cozzi's lawyers say they'll appeal, based at least partly on the severity of the sentence.