For six weeks, jurors had mostly been listening to evidence the government presented to prove its claim that Percoco, a longtime confidante and top aide to New York's Democratic governor, had accepted more than $300,000 in bribes from the businessmen who needed his help with state business.
Prosecutors made much of Percoco's use of the word "ziti" in emails to claim he knew he was accepting bribes. The term was used in the HBO mob drama "The Sopranos."
But defense lawyers said there was no evidence to show any bribes were made or that Percoco did anything unusual to help the businessmen.
Cuomo has not been accused of wrongdoing.
The deadlock claimed by jurors came as they wrote separate notes saying their personal hardships had become too great to overlook.
"I believe I cannot do this anymore!" wrote one juror.
"I regret to say I can no longer continue after today," wrote another.
That juror cited personal circumstances and the impasse, saying: "We have some very fundamental differences and nobody wants to compromise our own beliefs and/or process."
Assistant U.S. Attorney Janis Echenberg recommended one juror be excused and replaced with an alternate juror.
The judge, though, said she was not inclined to embrace that option because it would require restarting deliberations.