The fishermen, lodged in Karachi's Laandi Jail, were arrested by the Pakistani Coast Guards after they had mistakenly entered into its territorial waters while fishing off the Gujarat coast, officials at the Wagah border said.
"Indian prisoners are given a very bad treatment in Pakistani jails. We were even forced to clean the toilets," a fisherman said.
Others too claimed they were given similar treatment.
Boats of these fishermen, which are the main source of their livelihoods, have not been returned by the Pakistani authorities.
The figure was subsequently revised to 49 and later, 45 prisoners were freed.
India and Pakistan frequently arrest fishermen who mistakenly trespass into each other's maritime boundary and currently, 482 Indian prisoners are in Pakistani jails while 496 Pakistanis are in Indian jails.