The rescue, located in Humboldt County, is accused in court documents of taking in dogs from shelters for money while investigators believe some dogs were killed to make room for more.
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No charges have been filed against the rescue owner or employees. ABC7 Eyewitness News is not naming the rescue at this time.
Napa County Animal Shelter said in a social media post that all dogs from Napa County that remained at the rescue have been safely returned and are now available for adoption.
"These sweet dogs have been waiting a long time for the loving homes they deserve," the shelter wrote in a social media post over the weekend. "Since learning about the investigation, our team has worked closely with law enforcement and partner agencies to ensure the safe return of these animals."
Berkeley Animal Care Services (BACS) also said it recently got three dogs back from the rescue after learning of the allegations and contacting the facility.
In a post, BACS said the dogs, named Truffle, Bianca and Clem Smith, "came back thinner, with some bumps, bruises and in need of decompressing," but are now safe and receiving care.
Several Bay Area shelters, including Napa County, Oakland and Berkeley, had sent dogs to the rescue for years when they needed to clear space. Court documents say shelters paid hundreds of dollars per dog, trusting the rescue to care for the animals and adopt them out.
A search warrant affidavit obtained by ABC7 Eyewitness News says at least eight dogs were found in April buried on the property, some with bullet holes in their heads. The affidavit says the lead investigator believes at least one dog from Oakland was killed so the rescue could take in more dogs and more money.
The case is also getting attention from PETA, which says shelters need to do more to follow up with rescues.
"PETA's been sounding the alarm for years now, for years that you can't just trust everyone who calls themself a rescue," said Teresa Chagrin, PETA's animal care and control issues manager.
The investigation is ongoing. No charges have been filed at this time.