The historic site was earmarked to be developed into fourteen dwellings, until VCAT overturned the City of Greater Bendigo's planning permit in October.

Millson Developments' Scott Jackman said a stalled planning process has caused the building to lose its heritage.

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"It's incredibly frustrating to have things that you own disregarded, broken and destroyed," Mr Jackman said.

"Some of the things damaged are potentially irreplaceable."

The All Saints' Church, built in 1856, is the oldest church building in Bendigo.

Two of its vast number of stained glass windows and the associated school and Master's Residence, built in 1877, and linked by a Gothic archway, have been assessed to be of heritage significance.

Damage to the site is extensive and includes the removal of copper pipes, the destruction of numerous stained glass windows and graffiti.

In overturning council's planning permit, VCAT member Tracey Bilston-McGillen cited heritage preservation as one of the three key reasons for refusing to grant a permit.

"The time delays in this planning process and waiting for objectors' meetings has caused the destruction of the heritage they set out to preserve," Mr Jackman said.

"Vacant buildings become lost.

"What has happened here shows how important it is to have adaptive reuse of sites, to preserve history."

Bendigo police Sergeant Rod Davis said incidences of graffiti and wilful damage come in waves and penalties vary depending on the severity of damaged caused.

"It's one of those things that doesn't go away," Sergeant Davis said.

While properties each have their own unique challenges, Sergeant Davis said after hours security is crucial to minimise risk.

"Simple things that aren't cost prohibitive such as security screens for windows and sensor lighting can deter people," he said.

"Ensuring vegetation is trimmed and not overgrown and moving up the scale to putting in CCTV systems, which are of assistance to us if crime is reported to assist catching these people."

Mr Jackman said police have been called to the premises numerous times following new instances of vandalism.

"We made the site freely available to community groups to ensure passive surveillance but once they vacated, there have been persistent break ins during the past six to eight weeks," he said.

In its original planning application, Millson Developments proposed to build fourteen dwellings, with four of those to utilise the building.

"We are working as hard as we can to expedite the modification that fall out of the VCAT decision so with a bit of luck we will gain approval very soon," Mr Jackman said.

"As a city, if we are not open to how keep buildings in use and maintain their relevance, we end up with a loss of heritage altogether."