The new block-by-block approach will target what he calls COVID "micro-clusters."
Cuomo says the new plan can reduce the spread in hot zones.
A church in Kew Gardens will not be holding mass Sunday morning, with a sign on the door that says "it's closed" because it's in a hot zone area.
Meanwhile the State Department of Health had to issue a cease-and-desist order to stop a wedding in Williamsburg where more than 10,000 people were planning to attend that was scheduled for Monday.
The new method of targets the virus by block instead of county or borough in the hot zones. They will use red, orange and yellow to show where the virus is most concentrated by case and enforce closures or roll backs that way.
RELATED: Red, Orange, Yellow: Here are New York's new COVID cluster zones
Right now, the state wide positivity rate stands at 1.1% in the nine problem area zip codes in Brooklyn and Queens. It's over 4% on average, but in some of the red zones it's actually much higher.
Churches inside the red zone are allowed to open at 25% capacity. Some have decided to just remain closed.
The Brooklyn and Queens Diocese filed a lawsuit against the state asking for increased capacity higher than 25%, which was denied.
RELATED: Here's when NY movie theaters outside of NYC will be allowed to reopen
WATCH: Eyewitness to a Pandemic
MORE CORONAVIRUS COVID-19 COVERAGE
How coronavirus changed the New York region
Do you have coronavirus symptoms?
New York, New Jersey, Connecticut out-of-state travelers quarantine list
COVID-19 Help, Information. Stimulus and Business Updates
New York City
Westchester and Hudson Valley
Centers for Disease Control and Prevention on coronavirus
Submit a News Tip