The jury released a note after noon saying it had only been able to come to agreement on one of two acts it must decide before reaching a verdict on the racketeering charge.
"We have been unable to reach a unanimous verdict on all charges," the jury said. "We feel we are deadlocked."
The jury has been deliberating for six days. The panel had asked for some evidence to be read back as it deliberated over the last week, but the jury has not been particularly noisy in a courthouse where jurors can sometimes be heard shouting at one another.
U.S. District Judge Shira Scheindlin encouraged the jurors to give it another try, saying the case would likely have to be tried again and it was unlikely that another jury would be better able to judge the evidence than it was. Two previous juries in the last year wound up deadlocked, with resulting mistrials.
"I know it's been long, but there's still no hurry," she said, before they returned to a room adjacent to the courtroom to have lunch and resume deliberating. "I ask you with great respect that you continue your deliberations, and I await your word whatever it may be."
From the start, the jury has sought evidence aimed at deciding whether Gotti quit the Gambino crime family before July 1991, as he claims. If so, a five-year statute of limitations would have expired before prosecutors brought new racketeering charges in 2004.
Prosecutors say the jury should conclude Gotti continued to receive mob money after 1999 and thus was part of a racketeering conspiracy.
His defense lawyers say Gotti paid a large fine when he pleaded guilty to a racketeering charge in another case in 1999 and was permitted to keep the property and businesses that remained, regardless of where the money originated.
Gotti has also been accused of ordering two 1992 attacks on radio talk show host Curtis Sliwa, including one in which Sliwa was shot twice before he escaped out the window of a car.
Prosecutors have said Gotti was retaliating for on-air attacks against his father, John Gotti, who was sentenced in 1992 to life in prison without parole. He died in prison in 2002.
If convicted, Gotti could face up to 30 years in prison. He is free on $7 million bail.