(Warning video may be disturbing to some viewers.) Video shows the officer sitting on and punching the police dog.
Vacaville Police say the K-9 was not returning a toy and got aggressive -- which prompted the officer's violent response.
Protesters today called on the department to take action against that officer.
"Police dogs are police officers. If one cop is beating up another cop, he should be fired," one protester said. "Any other time an officer would have been put on leave right away."
But the city says the investigation is still in progress.
"The city of Vacaville is not making any excuses. We're not justifying any behavior. But we are investigating the incident thoroughly to make sure that whatever changes are neccessary -- that we're going to make those changes to make sure nothing like this happens again," said Kris Concepcion, Interim Vacaville public information officer.
Vacaville Police say the K-9 has been taken away from the officer, but that officer is still working.
WATCH: 'The dog was yelping': Video shows Vacaville officer punching K-9 partner
The San Francisco SPCA issued a statement Friday condemning what the organization described as "Vacaville animal abuse," regarding a video that went viral on social media this week depicting a Vacaville police officer punching his K-9 partner during a training exercise.
After the video circulated on Twitter and Facebook, the city of Vacaville announced Wednesday that it has undertaken what it described as "a thorough investigation of the incident," has separated the dog from the police officer and is reviewing its canine training program.
Police say the canine has since been examined by a veterinarian and shows no signs of injury.
In response to the video, "the San Francisco SPCA, being a leader in dog behavior and training, would like the public to know that physically threatening or harming an animal is never acceptable, regardless of the animal's behavior," the organization said Friday.
The organization's vice president of rescue and welfare said being aggressive toward a dog can cause problems.
"It's a misguided belief that dogs need to be dominated to be trained. The idea that a person must assume the 'alpha' position pervades our society and has significantly damaged the welfare of our canine companions and put many handlers at risk for serious injuries," said Jeannine Berger of the SPCA.
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"Being aggressive toward your dog will often cause your dog to become more fearful, anxious and potentially aggressive," said Berger, who is a veterinary behaviorist. "This popular belief is causing serious harm to pets and working dogs alike. It hurts our relationship with our dogs and causes more problems than it solves."
Earlier, PETA said the incident isn't training, but "abuse."
The City of Vacaville also said Wednesday that it has retained an independent third party with expertise in police canine training to review the incident, as well as the police department's policies and procedures and canine training program.
"Once the review is complete, the city will take appropriate action - including any necessary discipline and/or training, as well as any needed changes to policies and procedures to ensure the police department's canine program is in line with the industry best practices," the city said.
Bay City News contributed to this report.