The shooting was reported at the restaurant in the 300 block of Portion Road just before 1:30 p.m.
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Officials say there was a dispute between two people who ran away from the restaurant when police arrived.
A male is being treated at a local hospital with a gunshot wound and it is believed he was involved in the altercation at the restaurant.
Authorities say the incident was not random and multiple people are in custody, including the suspected gunman who was arrested within 10 minutes of the shooting.
At least 20 people were inside the restaurant at the time of the shooting -- including a child in a high chair -- but fortunately no bystanders were injured.
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Officials said it was a close call.
"I want to reassure the public that this incident was a targeted shooting, this is not something where the public has to be concerned that there is someone out there who is committing a random shooting -- this appears to be targeted," Suffolk County Executive Steve Bellone said.
Sachem schools were placed on lockdown immediately following the incident.
The schools locked down around 2 p.m. included Cayuga Elementary School, Hiawatha Elementary School, Nokomis Elementary School, Wenonah Elementary School, Samoset Middle School, Seneca Middle School and High School North.
The lockdown was lifted just before 3 p.m.
WATCH: Police briefing on IHOP shooting investigation
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