Being prosecuted for a series of thefts and robberies, Fernandes reportedly abused one Romeo Britto, a hotel owner from Siolim village, when the latter had come to depose against him on Thursday.
The gangster was being escorted back to the lockup after the hearing when he turned back to the court room and threatened the witness.
Britto has lodged a complaint with Mapusa police station about the incident and has sought protection.
The gangster is notorious for daring jailbreaks and has escaped five times, police said.
Recently, he had attempted to commit suicide in judicial lock up by consuming some tablets.
A senior police officer attached to Mapusa police station said the complaint of the witness was being investigated.
"Next time we will make sure that the gangster and witnesses don't come face to face," he added.