Police said the fight between criminal gang members detained in the jail erupted around 6:30 a.m. and lasted for only 10 minutes.
Two inmates died while being treated at a local hospital, police added.
Manila City Jail spokesperson Senior Inspector Jayrex Buestinera said 34 inmates were also injured in the incident triggered by argument over a bed space in the jail with a congestion rate of 370 percent.
He said nine inmates who sustained serious injuries were taken to a hospital for treatment while the other 25 detainees were treated at the city jail infirmary as they only sustained minor wounds.
A temporary lockdown was imposed in the jail in the wake of the incident, he added.