Heat stress has killed almost a third of an eastern Victorian town's native flying fox population, after extreme weather on Friday.

Victoria's Department of Environment, Land, Water and Planning (DELWP) declared a natural emergency on Friday after officers found dead grey-headed flying foxes near Bairnsdale.

On Friday temperatures soared to almost 46 degrees Celsius in East Gippsland, about 300 kilometres east of Melbourne, accompanied by strong winds.

The department temporarily closed the Mitchell River walking track near nesting areas of the animals at Bairnsdale, to try to protect the flying foxes.

But it did little to help the endangered bats, and authorities estimate about 1,400 of the animals perished near Bairnsdale, almost a third of the town's flying fox population.

Another 900 flying foxes were found dead near Maffra.

Mass deaths unprecedented in Victoria

DELWP spokesman Peter Simpson said the mass deaths were unprecedented in eastern Victoria.

More than 2,000 flying foxes perished because of extreme heat conditions in East Gippsland. ( Supplied: Friends of Bats and Habitat Gippsland )

"We have had grey-headed flying foxes impacted on before from heat events, but certainly not to the extent we have experienced over the last couple of days," he said.

"It was a prolonged period of temperatures up around 46 degrees across Maffra and Bairnsdale, also accompanied with low humidity and hot drying winds.

"And unfortunately, as a result we had a number of grey-headed foxes impacted at both sites."

He said the department estimated about 5,000 flying foxes were nesting near Bairnsdale before the devastating mass deaths.

It comes about a month after an extreme heatwave in Far North Queensland killed about 23,000 spectacled flying foxes, which is about one-third of the species in Australia.

Along with the spectacled flying foxes, the grey-headed flying fox species is also endangered, and classified as 'vulnerable' due to a significant decline in its population as a result of loss of habitat.

'A real disaster'

Wildlife carer Lorna King with a young flying fox which survived the heat stress event in East Gippsland last week. ( Supplied: Friends of Bats and Habitat Gippsland )

Bairnsdale wildlife carer Lorna King assisted the department to collect the dead and dying bats last week, and said the scale of the tragic heat stress event was enormous.

"I've never seen [deaths on] a scale like this. This is just horrific," she said.

"It's a real disaster; it was such a sad sight to see."

But there was a glimmer of hope for Ms King, after they were able to save four injured animals, including a very young female.

She said the baby grey-headed flying fox, which she estimated to be about 15 to 16 days old, was found among a number of dead young flying foxes.

"In all of this horror it is lovely to think one little girl survived, when all the other babies were dead," Ms King said.

Ms King nicknamed the young flying fox "Pip" and the animal has been sent to Melbourne for specialist care.

Friends of Bats and Bushcare president Laurence Pope said bat colonies across Victoria were affected by the heat event on Friday.

"This is the second heat event we've had this year, the first was on January 4," Mr Pope said.

"I buried 56 pups down at Yarra Bend on that day who succumbed to heat stress.

"While bats have evolved to manage heat stress, they can't manage [the] successive days and increased frequency of extreme heat that seems to be occurring across time," he said.

Just a few days before the mass deaths, flying foxes were active at Bairnsdale. ( Supplied: Friends of Bats and Habitats Gippsland )

Editor's Note (29/1/19): This story has been amended to clarify that almost a third of Bairnsdale's native flying foxes were found dead, not a third of eastern Victoria's.