The US Army Corps of Engineers has suspended the use of Nationwide Permit 21 in six states in the Appalachian region.
NWP 21 is used to authorise discharges of dredged or fill material into water for surface coal mining activities.
The suspension is effective immediately and applies to the states of Kentucky, Ohio, Pennsylvania, Tennessee, Virginia and West Virginia.
Companies proposing surface mines in these regions will have to obtain an individual permit from the US Department of the Army under the Clean Water Act.
National Mining Association president Hal Quinn said he was worried the decision could slow job creation in the region and add further uncertainty to the permitting process.
Surface mining is frequently opposed by environmentalists who say dumping of earth and rocks pollutes water systems.