Police were called in to quell a "disturbance" involving about 100 inmates of the jail in Lucena city, said regional police spokesman Chief Superintendent Serafin Barreto.
He said police shot at and killed four inmates.
The prison, about three hours' drive south of Manila, holds 845 inmates on trial for various crimes, he said.
"We're sure that the bullets came from the policemen," Barreto added.
The authorities were forced to fire back at the prisoners, some of whom had "improvised" firearms, Barreto said without explaining how the inmates had acquired the weapons.
More From This Section
"Instead of heeding (police warnings) they (prisoners) threw stones and shot at the elements of the Special Tactics and Response and Bureau of Jail Management and Penology," Sindac said.
The authorities "had no other recourse but to retaliate", Sindac added.
Barreto said the disturbance was triggered by prison officials' plan to transfer the leader of a prison gang into another cell block.