The rollback, announced in a memo by the US Fish and Wildlife Service, will end a two-year ban from the Obama-era brought in following a lawsuit by environmentalists.
Limited agricultural activity is permitted on some refuges by law, including cooperative agreements in which farmers can grow certain crops to produce more food or improve a habitat for wildlife.
Campaigners have said the lifting of restrictions poses a grave threat to pollinating insects and other creatures relying in toxin-free environments.
“Industrial agriculture has no place on refuges dedicated to wildlife conservation and protection of some of the most vital and vulnerable species,” said Jenny Keating, federal lands policy analyst for the group Defenders of Wildlife.
Previously, the US had prohibited the use of neonicotinoid pesticides, or neonics, on wildlife refuges, in conjunction with genetically modified organism (GMO) crops, engineered to resist insect pests.
Neonics are a class of insecticides tied by research to declining populations of wild bees and other pollinating insects around the world.
Rather than continuing to impose a blanket ban on GMO crops and neonics on refuges, Fish and Wildlife Service deputy director Greg Sheehan said in a memo that decisions about their use would be made on a case-by-case basis.
Mr Sheehan said the move was needed to ensure adequate forage for migratory birds, including ducks and geese favoured and hunted by sportsmen on many of the nation's refuges.
US interior secretary Ryan Zinke, whose department oversees the Fish and Wildlife Service, has made expansion of hunting on public lands a priority for his agency.
Sheehan wrote that genetically modified organisms have helped “maximise production, and that neonicotinoids might be needed "to fulfil needed farming practices.”
The move is the latest in a series of environmental restrictions introduced during Barack Obama’s presidency to be reversed under his successor Donald Trump, who has pledged to roll back government regulations.
In a 2014 Obama administration memo announcing plans to phase in the ban, Jim Kurth, head of the refuge system, wrote that seeds treated with neonics give rise to plants whose tissues contained compounds that could harm “non-target” species.
He also said, “refuges throughout the country successfully meet wildlife management objectives without” GMOs or neonics.
Mr Sheehan's memo named more than 50 national wildlife refuges across the country where the revised policy now applies. The entire system consists 560 refuge areas encompassing roughly 150 million acres across the United States.
Additional reporting by Reuters
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