The operation, centered in the Humboldt County town of Fortuna, involves the Humboldt County Sheriff's Office, the FBI and several state agencies.
In a statement released this week, the sheriff's office said investigators have determined that hundreds of dogs were transferred to the rescue by private citizens and animal shelters and that "a significant number of those animals have not been accounted for."
RELATED: Bay Area shelters cut ties with rescue after records claim dogs found shot, buried
Authorities said dozens of dogs have been recovered during the excavation, many of them with microchips.
The investigation began after a neighbor uncovered a burial pit containing eight dogs with apparent gunshot wounds.
"I hope it will be the beginning of a change where the animals will be removed from and placed into legitimate rescues where they find actual loving homes," neighbor Jennifer Raymond said.
More than two months after the investigation began, no charges have been filed against the owner or any employees. ABC7 Eyewitness News is still not naming the rescue.
The rescue remains open and operating, and the investigation remains active.
The investigation also follows reporting on a search warrant affidavit alleging the rescue accepted dogs and money from shelters across California under agreements that the animals would be cared for and rehomed.
Investigators allege some dogs were instead killed to make room for additional animals.
For a third consecutive day Thursday, excavators searched the property as residents watched the operation unfold.
"You cannot really put into words what exactly it smells like. The closest thing I think of is a pile of dead deer," Humbolt resident Jaiden Kilby said.
Berkeley and Oakland were among the Bay Area shelters that sent hundreds of dogs to the rescue before later cutting ties.
RELATED: Bay Area shelters retrieve dogs from NorCal rescue accused of shooting, killing animals
Legal experts said the lack of charges does not necessarily indicate that none will be filed.
"I wouldn't take the fact that it's been a little while and charges haven't been filed as any indication that they won't be," said Matthew Liebman, a professor of animal law at the University of San Francisco.
Liebman said animal cruelty investigations can be difficult to prosecute because of the nature of the evidence.
"Animal cruelty cases can be especially difficult to charge and prosecute because there are unique evidentiary challenges... the animals themselves can't testify," Liebman said.
Animal law attorney Bruce Wagman said one of the most alarming allegations in the case may not, by itself, constitute animal cruelty under California law.
"To euthanize an animal in California by a bullet, that alone is not animal cruelty," Wagman said.
Wagman also noted that even if investigators were to discover additional buried animals, animal cruelty charges would not be automatic.
Investigators have said hundreds of dogs sent to the rescue remain unaccounted for.
In addition to potential animal cruelty allegations, legal experts said the investigation could involve possible fraud, conspiracy and nonprofit law violations.
Updated excavation numbers are expected Friday.
The owner has repeatedly denied allegations that dogs were killed to make room for more animals.