So far five cases have been reported, and several others have been tested and are awaiting results.
The alert includes five ZIP codes: 10027, 10030, 10035 and 10037.
Health officials are testing water samples in the area to try and find the source.
"Any New Yorkers with flu-like symptoms should contact a health care provider as soon as possible," said Deputy Chief Medical Officer Dr. Toni Eyssallenne.
People only get sick by breathing in water vapor containing Legionella bacteria, and the disease is not transmitted from person to person.
Individuals at higher risk include those 50 years old and older, cigarette smokers, and people with chronic lung disease or compromised immune systems.
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