The Moorabool Shire Council was successful in obtaining an interim enforcement order at the emergency hearing.
Member Dalia Cook handed down the order, which said the couple must cease using their property for the purpose of keeping more than five dogs without a planning permit.
They have have also been forced to remove four dogs from the property by March 10.
The Paxtons came under scrutiny after graphic photos taken by Animal Liberation Victoria during a secret raid were made public last month.
The images revealed more than 30 dogs living in squalid conditions in small pens surrounded by their own faeces and rotting meat.
Council made an urgent plea to VCAT last week to grant an interim enforcement order, which would allow the council to shut down the site.
The hearing came after a report submitted to council last year revealed up to 59 dogs were kept on the property at one time, prompting neighbour complaints.
It is understood they now have just nine dogs, with dozens of them given away in recent weeks.
Mr Sherwell said while the Paxtons agreed to reduce the number of dogs , they could not come to an agreement regarding the structures on the property.
The council wants them removed, as they were erected without a planning permit, but the Paxtons claim they will be used as aviaries.
The Paxtons also claim they will require the use of some of the structures to house the five remaining dogs.
Moorabool chief executive officer Robert Dobrzynski said while council was happy with the outcome of the initial hearing, it would continue to investigate the matter.
Council staff will inspect the property on Thursday to ensure the Paxtons have removed the four dogs in question.
Ms Cook explained to the Paxtons that should they breach the order, they would face severe consequences.
A second hearing will be held on March 16 to determine whether existing structures should be removed from the property.
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