The deputy was responding to reports of an aggressive dog running loose near the elementary school, officials said.
The deputy followed the Rottweiler mix to a home on Lakeview Road, while he was speaking with the homeowner, the dog ran towards him from the side of the house, said an official with the Sheriff's department.
The deputy fired twice, hitting the animal both times.
The dog ran away from the deputy and into a culvert about 120 feet long and 3 feet in diameter, said San Diego County Animal Control's deputy director John Carlson. Officers had to crawl in and retrieve the animal.
Animal control officers left a notice on the dog's owner's door to let them know where the dog was taken, but they have not stepped forward yet, Carlson said.
This isn't the first time animal control officers have had to deal with complaints about this dog or other dogs from the same household, Carlson said.
This was also the third time deputies were called to neighborhood, because the dog was running loose.
Officials say the deputy will not be placed on administrative leave. The case is still being investigated.
This is the second time a deputy has shot a dog in the past two weeks. A deputy serving a search warrant in East County, shot and wounded a pit bull who tried to attack him while he was executing the warrant.