The Food and Drug Administration is suing the city in an effort to block its policy of labeling calories in restaurants and supermarkets.
The city rule was adopted in 2015 and was set to go into effect next Monday.
It would require chain stores like 7-Eleven and Whole Foods to post calorie information on their menus.
The FDA says it's in the process of setting a uniform national standard and pushed their deadline for that back to 2018.
They say they believe local governments should be stopped from adopting any rules that conflict with federal regulations.
Health Commissioner Dr. Mary Bassett calls it short-sighted.
"I was surprised that they've taken it upon themselves to take such an eager role in aligning with industry, which has fought the city in our efforts to provide healthier food for our residents," Bassett said.
"It's not about being on a diet. It's about eating more healthier now," said one New Yorker. "And people are so obese and the children are so obese. So when we go into any store, any establishment, we would like to know our intake on what we're taking."
A judge will hear arguments from both sides on Wednesday.