Additional fencing and hoardings bearing the name of a demolition company appeared in recent days and the electronic sign, which also has a controversial history, was removed on Wednesday as contractors moved in.
The hotel has been derelict since a fire ripped through it in 2007.
It has been linked over the years to disgraced former Shepparton councillor Milvan Muto, who engaged in a series of battles with the council over the future of the site.
The council confirmed in a statement on Thursday that it had issued a 90-day demolition order for the building.
“An Emergency Order has been issued in accordance with the Building Act for full demolition of the Shepparton Hotel. Due to privacy reasons, council officers are unable to comment further at this stage,” the statement read.
The hotel has been subject to a number of stop-work orders following the removal of bricks, particularly from the internal walls, in recent years.
In July last year the council declared the building a risk to life and property and set a deadline for urgent works to shore up the building.
At the time, the council erected a temporary fence around the site to prevent access and closed the footpath. Late last year more permanent structures were put in place to prevent pedestrians accessing the area.
A structural engineer who assessed the building determined that demolition and removal of internal brick walls had compromised the building.
The demolition order was issued after the owners failed to undertake any remedial works.
The hotel has had a controversial history during the past 15 years, with the council issuing stop-work orders to try to halt the removal of bricks and prevent a slow demolition of the building without a permit. In the end, the council has accelerated that demolition to protect public safety.
In its current state the hotel was also a candidate for new punitive council rates of 360 per cent of the general rate that can be applied to derelict buildings.