State Minister for Sustainability, Andrew McNamara, told Parliament yesterday the decision follows a recent finding from the Animal Welfare Advisory Committee that shooting flying foxes is inhumane.

"The protection and management of flying foxes is an ongoing matter of public interest," Mr McNamara said.

"They play an important role in the maintenance of biodiversity as a plant pollinator, but they also feed on fruit crops, particularly lychees and rambutans."

Shooting of flying foxes for crop protection has been authorised by the Environmental Protection Agency under Damage Mitigation Permits, but only for strict numbers agreed to by the Commonwealth on an annual basis.

But Mr McNamara says no further permits will be granted in Queensland for shooting flying foxes after September 1.

"Thankfully, the number of permit applications has been declining in recent years, as growers recognise that the only secure method of protecting their crops is by netting," he said.

"I'm advised the vast majority of growers have moved to netting."

But farmers are still unhappy with the decision, with lobby group Growcom warning that it will lead to severe crop and economic damage.

Growcome chief executive, Jan Davis, says the lack of consultation with Queensland's $1.1billion fruit industry on the issue was a disgrace and accused Primary Industries Minister Tim Mulherin of failing to represent growers needs in the government decision-making process.

"The Environmental Protection Agency and the Minister's Office have a long history of keeping the fruit industry in the dark on matters of significance to it," Ms Davis said.

"We are extremely concerned at the Minister's lack of understanding of the impact of this decision and invite him to undertake a farm tour to ensure he is properly informed of the management issues growers face, even on netted or partially netted properties.

"The immediate withdrawal of damage mitigation permits threatens the spring and summer fruit harvest this year as growers will have no time to find alternative crop protection options."

Ms Davis said damage to fruit crops by flying foxes is particularly severe for the stone fruit, lychee, longan, rambutan and table grapes commodities.

"While netting is increasingly used across all fruit growing regions, the fruit industry continues to be highly reliant on damage mitigation permits to shoot flying fox scouts and protect un-netted areas of their crops from mass-scale predation by local flying fox populations," she said.

"Permits are not a primary method of crop control - they are last resort measures. Taking out a handful of flying fox scouts is an effective control mechanism - and doesn't result in large numbers of animals killed in total."

According to Growcom, less than 1500 animals were authorised by the State Government to be killed in 2005/2006, which is no threat to overall populations.

"We estimate that without access to damage mitigation permits, fruit growing regions that come under strong predation from flying foxes could lose 60-100pc of crops, causing massive financial damage to farming businesses, local communities and regional economies," she said.

Mr McNamara said the Queensland Rural Adjustment Authority would provide low-interest loans to help those affect switch to net protection from flying foxes.

"Of course, the use of nets incurs a cost, but that is offset by more and better quality fruit, less time spent sorting and packing, no time spent patrolling orchards at night and more reliable production yields," he said.