Wildlife carers say they cannot continue to nurse injured kangaroos back to health only to risk having them shot by a neighbouring farmer once they are released.

Marcus Ward, owner of the Pastoria East Wild Life Shelter, says he will have to close his doors after 30 years.

He said he was left with little choice after the Department of Environment, Land, Water and Planning decided not to prosecute the neighbouring property owner for animal cruelty, after kangaroos were shot in the body and left to bleed to death.

"We saw kangaroos that we had raised and nursed ourselves for months, dead," Mr Ward said.

"It's been an appalling relationship between our centre and the department and we put up with it for so long for the animals, but they've made it clear they don't want us around.

"It's been 30 years ... it's absolutely devastating."

Mr Ward said he suspected the animals currently in his care would be killed once they were released. He is hoping they can be transferred to other shelters.

The department began investigating the neighbouring property owner and suspended his licence to cull pests on his land after Mr Ward and his fellow carers took photographs of 23 kangaroo carcasses.

The carers claimed some kangaroos died from body wounds, instead of being shot in the head, and two joeys were allegedly left to die in the pouches of their mothers. Some of the shot kangaroos had been nursed back to health after being injured in last year's Lancefield bushfire.

But in a statement Tuesday the department said there was "insufficient evidence" and "no legal basis" for prosecution and agreed to reinstate the man's culling licence.

"The new conditions require the holder to engage a professional shooter, give DELP 48 hours' notice before commencement of shootings and provide documentation to DELP after the shootings have occurred," the department said.

Mr Ward said he was "gobsmacked" at the decision.

"This is a sorry event from start to finish … there was plenty of evidence the rules had been grossly breached," he said.

"We absolutely support the right to farm or protect pastures and crops, but all non-lethal methods must first be pursued such as putting up fences."

Peter Tuohey, president of the Victorian Farmers Federation, said kangaroos could cause severe damage to properties.

"They certainly are a pest at times. By grazing on farmer's property they destroy crops and can be damaging to pastures ... [but] we don't support the inhumane culling of kangaroos."