The country's health department launched an investigation at the neonatal ward of the Ospital Ng Makati, in the financial district of the Philippine capital, after 25 babies died in similar circumstances in May.
The national health department has called the death rate at the facility "alarming", amid concerns that the blood infection, known as neonatal sepsis, might have been spread due to unsanitary conditions.
Municipal health authorities shut down the neonatal intensive care unit last week after the May deaths came to light, but the facility is still accepting emergency cases.
One baby admitted this weekend died of neonatal sepsis early Monday, said Eric Tayag, of the National Epidemiology Centre.
Tayag said the results of the probe would be available in 10 days.
"If we find negligence on the part of hospital staff and personnel, the city government will definitely file the proper cases against them," Makati Mayor Jejomar Binay said.
In May, the hospital reported 25 deaths out of 45 babies suffering from neonatal sepsis -- out of a total 273 deliveries that month.
In the first four months of the year, the hospital handled 16 cases of neonatal sepsis but did not report any deaths.
Two years ago, a Manila hospital was forced to close its neonatal unit after seven babies died of sepsis.