The airline said the passengers were getting medical attention "as a precaution".
A federal Customs and Border Protection spokesman says the sick passengers had been attending the hajj in Mecca, Saudi Arabia.
According to Phillips, the sick passengers are headed to the hospital.
- Emergency personnel responded to reports of sick passengers aboard an Emirates flight arriving at John F. Kennedy Airport on Wednesday morning.
The plane, thought to be an Airbus A380 containing at least 500 passengers, is said to have been quarantined.
All 250 passengers and crew on the flights were held for a medical review and the Centers for Disease Control and Prevention was notified to investigate.
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The Centers for Disease Control and Prevention is evaluating ill passengers aboard two global flights that arrived in Philadelphia from Paris and Germany Thursday afternoon, a CDC official said.
Eric Phillips, a spokesman for Mayor Bill de Blasio, tweeted on Wednesday morning that the flight had stopped in Mecca, which is now experiencing a flu outbreak.
Video footage from inside shows confusion on board the plane, as officials try to clear the aisles and keep passengers in their seats.
The Port Authority of NY said the plane was taken to a separate park of the airport.