California authorities unearthed at least 117 dogs in “various states of decomposition” on Friday, many of which appeared to have been killed by gunshot, as part of an ongoing investigation into an animal rescue organization.

Limited time: Save 25% on NBC News subscription

Get exclusive reporting, live Q&As and ad-free reading.

The bodies were discovered during a search of Miranda’s Rescue in Fortuna, California, according to the Humboldt County Sheriff’s Office. Officials had been granted a warrant that included excavation of the property for evidence that dogs had been buried in “mass graves.”

The 117 canine remains were those found mostly intact at two sites, the sheriff’s office said. Nearly two dozen skulls, “hundreds” of bones, and 600 dog collars were also recovered on the property.

Humboldt County Sheriff William Honsal thanked the law enforcement teams and forensic veterinarians who assisted in the recovery. In a statement, he noted that the investigation is “just getting started.”

“The determination all of these professionals showed while working through this horrific scene is something we will not forget,” Honsal said.

NBC News was not able to reach Shannon Miranda, the founder of Miranda’s Rescue, by phone on Sunday. She did not immediately respond to an email requesting comment.

The sheriff’s office said in a news release last week that it had been contacted in April regarding allegations of fraud, animal abuse and animal cruelty at the rescue, and that the case had been assigned to the Major Crimes Division.

An initial search warrant was executed on May 1, at which time officials seized evidence related to the investigation. Investigators also determined that a “significant number” of animals surrendered to the rescue had not been accounted for.

A second search warrant, executed Thursday, led to the recovery of the canine remains.

Forensic veterinarians were able to examine 71 of the bodies on-site Thursday but did not have time to reach the remaining 46. A preliminary examination — including X-rays of the remains — found that “many of those animals showed evidence of bullet fragments.”

Investigators are working to identify dogs that were microchipped.

Other remains were found “in advanced stages of decomposition” and were deemed too severely deteriorated to be removed from their burial site, the sheriff’s office said.

This investigation is expected to be lengthy, the sheriff’s office cautioned in a statement to the public.

“The Humboldt County Sheriff’s Office understands the public’s desire for accountability and justice,” it said. “However, it is our responsibility to conduct a complete, impartial, and legally sound investigation while ensuring that the constitutional and legal rights of everyone involved are protected throughout the process.”

No charges were announced.

Miranda was not available for comment, but posted a statement on June 18 addressing “recent media coverage and online commentary,” on the rescue’s website. The statement described two incidents that had “drawn particular attention” both involving animals that were killed at the facility.

The first involved a dog that killed another animal and attacked a third; the second involved a dog that lunged at a stroller carrying a baby, according to the statement.

“These were not decisions made lightly and were based on my responsibility to protect both the public and the animals in our care,” Miranda wrote.

The statement also described Miranda’s Rescue is a no-kill shelter, meaning animals are not euthanized simply to free up space, but acknowledged euthanasia is sometimes necessary.

“Whenever euthanasia has been necessary, I have notified local authorities in advance, even when told that reporting is not required,” Miranda wrote. “I believe it is important to maintain a clear record of these difficult decisions.”