Indie was found with a broken neck and suspicious puncture wounds.

Police are investigating whether Indie was deliberately killed. Photo: Supplied

Police are investigating whether a dog's neck was deliberately broken in a case of animal cruelty in Gippsland.

The owners of the two-year-old Maltese shih-tzu found the body of their pet lying in their backyard in Traralgon last week.

The dog, named Indie, had a broken neck and suspicious puncture wounds.

A Victoria Police spokeswoman said Indie and another Maltese shih-tzu escaped from the home on High Street about two weeks ago.

The second dog returned home soon after, but Indie remained missing.

Last Friday the owners heard a dog yelping in their backyard and, when they went to investigate, found Indie's body.

Police are investigating whether the dog was deliberately killed.

"Detectives believe someone may have been taking care of the dog after it ran away and are appealing for anyone who may have located or seen a small dog over the past two weeks to come forward," the police spokeswoman said.

It follows the shooting of a four-year-old dog on the Mornington Peninsula this week.

Detectives were told that the daschund, named Levi, was found dead at his owner's property at Red Hill, east of Dromana, about 7.45 pm on Sunday.

The owner, Max Paganoni, returned home to find Levi dead when he went to feed his pet.

Mr Paganoni's other dog was not injured.

Mr Paganoni, a restaurant owner, said that Levi was still warm when he picked up the animal.

"I got the vet to check to make sure it was a bullet because I didn't want to accuse people of something that didn't happen," he told radio station 3AW earlier this week.

"The scariest thing is somebody is walking around with a gun and (is) happy to use it."

Anyone with information about the dogs' deaths has been urged to contact Crime Stoppers on 1800 333 000.