The landholder is one of the first four across Queensland to apply for the permit since the State Government reintroduced access to them.
To be successful landholders must prove they have attempted to move the bats on through non-lethal methods.
Farmers in the Lockyer Valley have previously expressed concern about the impact flying foxes have had on fruit crops.
The LNP promised to reintroduce lethal damage mitigation permits to deal with bat populations in the lead-up to the election.
However, Bat Conservation and Rescue Queensland have dubbed bat shooting as "inhumane and ineffectual, (and) shamefully cruel". A statement from the conservation group states shooting could lead to the inhumane death of infant bats.
"As fruit-ripening season coincides with flying fox birthing season, killing bats in orchards results in large numbers of baby flying foxes being orphaned and wounded.
"These defenceless babies are left to a slow and protracted death from dehydration, starvation and maggot and crow predation."
Environment Minister Andrew Powell said the changes were part of an agreement between the State and Federal Governments to address the issue of flying fox damage to crops, but stressed permits to shoot bats would only be an absolute last resort.
"This is not open season on flying foxes, these permits will only be issued to growers who can show that they have tried unsuccessfully to use non-lethal means of moving flying foxes away from their crops," Mr Powell said.
A spokeswoman for the department said urban colonies in Woodend and Gatton would not be considered for shooting.
To apply for a permit to shoot flying foxes applicants must meet specified criteria.
There must be "significant economic damage" or "a threat to human wellbeing."
There is an effective method of minimising the impact of the wildlife.
The proposed technique must be humane.
The impact of the activity will not detrimentally affect sustainability.