HARRISBURG — Pennsylvania’s state environmental regulators have agreed to take more precautions before they approve certain permits for oil and natural-gas drilling sites where well construction poses a pollution threat to some of the state’s highest-quality waterways.

The state Department of Environmental Protection agreed to the measures to settle a complaint by the Chesapeake Bay Foundation filed in 2009 that also asserted the agency had approved three deficient permit applications.

The settlement essentially reverses some steps the department took to speed up the permitting process for Pennsylvania’s booming natural gas industry.

The settlement, dated Wednesday, was approved by an Environmental Hearing Board judge. The resulting stricter review process could take up to 60 days. Currently, those permits can get approved in a matter of two weeks.

Under the settlement, the department will require the stronger review if well or pipeline construction poses the potential to pollute a high-quality waterway, or is on a flood plain or on a contaminated site near a waterway.