A home in El Cajon also was searched as part of the operation, she said. Authorities declined to disclose who owns the shops and the residence.
Among the confiscated animals were nearly 60 puppies, a number of rabbits, a 35-pound turtle and a 7-foot python.
"These animals have been transported (and) received full veterinary exams, and several have received medical treatment and surgery," said Randall Lawrence, law enforcement director for the San Diego Humane Society. "All of the animals are now being housed ... as potential evidence for the pending investigation."
None of the impounded pets were available for immediate adoption, as the investigation could be ongoing for months, Herwehe said.
Charges that potentially could result from the investigation include animal cruelty and neglect, as well as violations of state health-and-safety codes, according to Lawrence
"Any possible charges that may be pressed against the owner of these pet stores will be determined based on the evidence we collect from the public, along with the condition of the animals," he said.
A grassroots group that calls itself the San Diego Animal Defense Team has been protesting the stores since last August and filed complaints with the county, calling the businesses "puppy mills."