Mildura Council has defended the shooting of the six cats shortly after they were dropped at the shelter last week, saying they were feral and unable to be controlled.

But RSPCA president Hugh Wirth says the shootings are indefensible acts of cruelty and an animal should only ever be shot in an emergency situation, if it is suffering and needs to be put down immediately.

''This was not an emergency situation,'' Dr Wirth said. ''I'm completely outraged.''

The Mildura shelter had a vet available to administer lethal injections and with training in dealing with feral cats, ''if in fact that's what they were'', Dr Wirth said.

The RSPCA is investigating and the officer could face criminal prosecution under the Prevention of Cruelty to Animals Act.

Mayor Glenn Milne released a statement saying the officer acted lawfully.

''Whilst destruction of animals via gunshot is not normally the standard procedure, it can be performed in certain circumstances,'' he said.

''We regret that this has caused concern amongst the animal welfare community, however this is an accepted method that council can use. There were no malicious intentions by any member of staff.''

Dr Wirth said Cr Milne's defence of the killing made him ''as bad as the shooter''.

''Any manager in Mildura Shire who has permitted that ought to be fired as well as the shooter,'' he said.

The last known case of animals being shot in a shelter was in Horsham three years ago, he said.

Dr Wirth said such shootings often reflected an attitude that a bullet was cheaper than a vet.

A lethal injection would render a cat unconscious within about two seconds, while a gunshot could leave the animal suffering in pain for hours, he said.