The lockdown at Elmont Memorial High School was put into effect about 8:15 a.m. after a call about 30 minutes earlier from a woman who said she had seen a male teenager with a backpack and a green gun, WCBS-TV, New York, reported.
Police said the gun was probably a toy, but that they were taking the incident seriously.
By midday, Nassau County police guarded the school entrance as officers searched the building room by room. SWAT teams were visible at the front of the school.
The surrounding area was searched by helicopter.
Parents were alerted with "robo-calls." Students arrived about the time of the lockdown were sent home, officials said.
A parent said she had talked to her child inside the school who said students were huddled in their classrooms with the lights out.