Speaking during his daily briefing the governor said "We will stay on track by focusing on the hotspots."
Some of the areas with the highest numbers of cases of COVID-19 have been the Bronx, Queens, and Brooklyn.
"We know down to the zip code where the infection rate is higher than average. We will meet the need where it is greatest," added Cuomo.
As many as 400,000 employees are expected to return to work in NYC with the beginning of phase one.
"Remember that reopening does not mean that we are going back to the way things were. Life is not about going back. Nobody goes back. We go forward. It's reopening to a new normal. People will be wearing masks. People will be socially distancing," said Cuomo.
Mayor Bill de Blasio joined Cuomo via video conference a day after announcing that phase one would begin during the first two weeks of June.
"The last 90 days for all of us, a lot of long days for all of us," said de Blasio. "We are excited to get to the point of a restart for New York City.
During his daily briefing earlier in the day, de Blasio said that there had been 61 new hospitalizations for coronavirus in the past 24 hours.
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"Only five percent of those tested, tested positive in New York City. These are great indicators," added de Blasio.
As many as two million face masks will be distributed for free to businesses across the city during phase one and a hotline will be established to report concerns over conditions at places of employment.
Friday marked 90 days from the start of Cuomo's 'Pause' order to help curb the spread of the virus.