Toowoomba Regional Councillor Ros Scotney said The Pittsworth District Alliance made the application to the Department of Environment and Heritage Protection yesterday.
She said she hoped the application would be fast-tracked.
"On the form it said it would be April 2 before it (the removal) was enacted," Cr Scotney said.
"We are not happy with that.
"They (the flying foxes) have just got into plague proportions."
Cr Scotney said the plan was to use laser lights to frighten the flying foxes.
"They have to be set up to come on at 3am."
She said the option of loud music had been discussed, but was not sure it would be suitable in a residential area.
Mayor Paul Antonio and Member for Toowoomba South John McVeigh also visited the Short St area of Pittsworth at the weekend.
"Now we just have to wait for a response."