Authorities say a shipment of nine dogs from Missouri was rejected at a pet shop in Hicksville Wednesday because the owner thought they looked sick.
The SPCA was notified, and the dogs were seized.
They are now being cared for and checked by a veterinarian.
Officials said a second shipment was also seized at a shop in Mineola.
Detective Gary Rogers, with the Nassau County SPCA, said they are investigating and trying to stop a pipeline of dogs coming into the area and that the CDC has issued a health advisory for diseases that come from puppy mill dogs.
He stressed the pet stores did nothing wrong and are not under investigation.
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