Dr. Morse had a warning for New Yorkers, saying cases have declined, but "we're not out of the woods yet."
"This is not the time for New Yorkers to relax their efforts to protect themselves," she said.
More than 128,000 New Yorkers have tested positive for flu so far this season, which was more than what was reported at the same time from the past two seasons, according to the health department.
Officials say the virus continues to circulate at high levels and the best protection is vaccination.
The department on Thursday, slammed the Trump administration's decision to cut the number of vaccines recommended for children, including protection against the flu.
"In response to the CDC revised childhood vaccine schedule, we coordinated with New York State officials to send clear guidance to health care providers yesterday through the statewide health advisory network," said Deputy Chief Medical Officer Dr. Toni Eyssallenne.
What's especially concerning for officials is that they have seen a 6% decrease in childhood flu vaccinations this season compared to the last respiratory season.
Monique Drake and her daughter got sick this holiday.
"This time runny nose, headache, cough, and this tiredness," she said.
Still, she thinks the vaccine kept her out of the hospital this time.
"The last time I was so weak and I had to end up going to urgent care and getting all kinds of medicine," she said.
Others opted against the vaccine this season.
"I take my vitamins and I try to stay away from people as much as I can," said Mandy Joseph, who didn't get vaccinated.
Last month, the city saw a record amount of flu cases reported in a single week.
Health officials say it is too early in the season to say whether or not cases in New York City have peaked, noting that flu season typically lasts until May.
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