"We are seeing community transmission of the Omicron variant in the capital region," Health Undersecretary Maria Rosario Vergeire told a public briefing.
The region is an urban sprawl of 16 cities home to more than 13 million people.
The community transmission of the Omicron variant is characterised by a steep rise in cases, Vergeire said, adding that infections may peak from the end of this month to mid-February.
The ministry reported 39,004 new COVID-19 infections on Saturday, while active cases also hit a record, at 280,813.
With more than 3.16 million cases and nearly 53,000 deaths, the Philippines has the highest COVID-19 infections and casualties in Southeast Asia after Indonesia.