The Suffolk County Society for the Prevention of Cruelty to Animals says the horses taken from the Central Islip property on Sunday morning were in danger of dying.
A veterinarian says they were severely neglected and required emergency medical care.
SPCA officers say they've arrested a man in connection to the case and charged him with five counts of animal cruelty.
The horses are being cared for. If they can be stabilized they'll be placed in foster care pending the outcome of the case.