The days of a flying fox colony nestled among the high-rise buildings and bustling traffic in the centre of Cairns could be numbered, with plans to move them on.

Flying foxes in far north Queensland have had a tough summer, with a record-breaking heatwave late last year estimated to have wiped out more than 23,000 spectacled flying foxes, equating to almost a third of the species in Australia.

The local Cairns Regional Council has found a new area in the outer suburbs of the city and plans to place orphaned baby bats in a cage and lure the adults there by playing on their maternal instincts.

"In other places where they've had these facilities where they've cared for the bats, they've noticed the adult bats tend to congregate around that," Councillor John Schilling said.

Thousands of spectacled flying foxes dropped dead during the heatwave in Cairns. ( Supplied: David White )

"So we think if we can use them as a bit of a lure … we can solve a problem for the bats and for the city."

Permits from the Queensland and Federal Governments are still needed before any work starts, but Councillor Schilling said he was hopeful the application would be successful.

"We believe we're acting in the best interest of the city and the bats themselves, to secure their long-term future," he said.

"We're all of the view that no-one wants to see more losses; we need to reduce losses, and this is our best way forward."

Luring bats hard to make work

The plan by the Cairns Regional Council has been met with scepticism by a local bat conservation group.

Cairns Bats and Tree Society president Maree Treadwell-Kerr said the current health of the bat population could be a problem.

"We do agree that the CBD has become a dangerous place and this is because the trees were removed and they've been forced to roost in more unsuitable trees," Ms Treadwell-Kerr said.

"But we're opposed to actually causing them more stress considering they've suffered a food shortage as well as a heat-stress event in the last year."

The Cairns Bats and Tree Society is concerned more bats could be lost if moved. ( Supplied: David White )

The new area the council has in mind is in the suburb of Edmonton, which is more than 10 kilometres south of the city centre.

Ms Treadwell-Kerr said luring the bats to a specific spot so far away could cause problems.

"If you had a continuous vegetation corridor, you could move them down the vegetation corridor because that's the way they'll be going," she said.

"But there isn't, they're just going to go off and land in whatever trees there are and they could land in quite inappropriate parts of the city.

"There's always the risk of losing bats during a dispersal."