The Moorabool pair were ordered by the Victorian Civil and Administrative Tribunal to remove the dogs from their Beremboke property after they were found to be running a renegade puppy farm.

An Animal Liberation Victoria raid on the farm last month found dogs housed in appalling conditions, surrounded by rotting meat and their own faeces.

It is believed that at one time, there were up to 59 dogs housed at the property, without a permit.

A VCAT emergency hearing in Melbourne last week granted the Moorabool Shire an interim enforcement order, requiring the Paxtons to remove all but five dogs from the property by the end of Wednesday this week.

"Council compliance officers visited the Paxtons about 6.15pm Wednesday night and found four dogs on the property," Moorabool chief executive officer Robert Dobrzynski said.

"This is in line with the VCAT order."

There is believed to be a fifth dog that was not seen by officers, but this is unconfirmed.

A second VCAT hearing will be held on Tuesday March 16, where council will be pursuing the Paxtons over the use of the land for intensive animal husbandry for pigs and perhaps rabbits.

Council is also seeking an order for decommissioning the excess animal-keeping facilities, including a shipping container, and a permanent order regarding the dogs.