The dogs and cats were seized at a house in Scotch Plains overnight.
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Chihuahuas, Pomeranians and retrievers were among the 71 dogs kept in the basement of the home.
A dozen local shelters have assisted by taking in the pets and providing medical care.
The Plainfield Area Humane Society says it has 42 of the animals, while St. Hubert's Animal Welfare Center of Madison took in 40 others.
All are being continually cared for and evaluated by staff and will receive medical treatment if needed.
The Union County Prosecutors's Office is now investigating the activities at the home where the animals were found.
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Criminal charges could follow, and eligible animals will soon be available for adoption.
In the town of Scotch Plains, there is an ordinance preventing pet shops from purchasing animals from puppy mills, with most being sold over the internet or in parking lots to potential dog and cat owners.
"Puppy mills are inhumane commercial breeding operations that put profit over the health and well-being of animals," St. Hubert's said in a statement. "According to the Humane Society of the United States - NJ, nearly 140 New Jersey towns have passed anti-puppy mill ordinances to protect consumers and animals."
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