Reports initially described some of the 500 passengers on the Airbus A380 as being "seriously ill", coughing and suffering with a fever.
The flight, EK203, arrived from Dubai on Wednesday morning at around 09.15, with “at least” 100 passengers feeling ill, NBC New York reported.
However, an Emirates spokesperson has since said "about 10 passengers" were taken ill.
The aircraft was pictured surrounded by emergency service vehicles and passengers told to remain in their seats.
A team from the Centers for Disease Control and Prevention is currently investigating.
"On arrival at JFK, as a precaution, they were immediately checked by local health authorities and those needing medical attention will be attended to," the airline said.