"That's very, very untrue," Donaghy told USA Today in a telephone interview.
National Basketball Referees Association spokesman Lamell McMorris said a man identifying himself as Donaghy made calls July 30 to McMorris' Perennial Strategy Group, a Washington consulting firm, allegedly threatening bodily harm.
Donaghy was sentenced July 29 to 15 months in a Pensacola, Fla., federal prison for wire fraud and transmitting betting information.
McMorris said the caller threatened to "have someone hurt" if the referees' association did not stop "spreading lies to the media,"
The person emphasized his anger toward McMorris for calling him a "scoundrel" in a statement after Donaghy's sentencing, USA Today quoted McMorris as saying.
"He reiterated that he was tired of 'taking it' and was upset and had info that he had not released," McMorris said.
Reached on his cell phone, Donaghy told the newspaper he made no calls to the association.
"I did not threaten anybody, nor would I ever threaten anybody," he said.
Donaghy resigned from the NBA and the union after being indicted last summer. He reports to prison Sept. 23.