Some 9,731 prisoners in the country were freed as coronavirus disease (COVID-19) affects jam-packed jails infecting both inmates and corrections personnel.
The order allows the release of those awaiting trial for the reason they could not afford bail.
Among those with infected cases are Quezon City Jail and two other jails in Cebu.
Overcrowding has become a problem after President Rodrigo Duterte launched the drug war in 2016. As thousands were sent to prison, cells are filled five times more than its desired capacity.