The owner and operator of the kennel, Christina Fay, 60, of Wolfeboro, was arrested on two misdemeanor counts of animal neglect.
She is due back in court on August 2.
Police said the case is "about reckless conduct, abhorrent behavior toward animals over profit, and scofflaw attitude about business practices".
No one answered the intercom at the gated compound where the dogs were seized and a man entering the property wouldn't give his name but said Fay was not there. The dogs were safely transported to a temporary emergency animal shelter, the society said in a statement.
According to WMUR, 75 of the dogs were rescued from a location in Wolfeboro, while nine more were rescued in Bartlett.
"When we walked in, the smell of ammonia was so overwhelming and there was waste and feces all over the house, on the walls, it was just really heartbreaking", Hamrick said. "I have never seen anything like this in my career in law enforcement or in my career in the military".
Hamrick said while many law enforcement personnel were wearing hazmat suits complete with booties, she could not wear the booties for fear of slipping on the feces and urine that covered the floor.
Hamrick, who 5-feet. 3-inches tall, said some of the pony-sized dogs could look her in the eye and some tipped the scales at more than 300 pounds.
"There is a perception that puppy mills happen only in the Midwest and the South".
Police said they first arrived to the property on May 9 after animal neglect allegations.
There was limited access to food or water.
Some dogs were starving, with the outline of their bones poking from their fur, others were suffering from serious eye and skin infections.
The question everyone has been asking, "how can they foster or adopt these dogs?"
The dogs will not be available for adoption until the case against Kay is heard as they are evidence in the criminal case. In the past, she has seen cases take anywhere from three to 18 months. "I'm not ashamed to tell you that I was upset".
Lindsay Hamrick, New Hampshire state director for The HSUS who was on the scene, said: "It's astonishing that such cruelty can occur and I'm so relieved that these animals are now safe and in the hands of people who will provide proper care for them". But the financial burden of long-term care for these dogs required additional assistance.
The website shows photos of dogs in open grounds or in seemingly clean areas within the home.