CHARLESTON — The U.S. Army Corps of Engineers wants Congress to exempt it from a South Carolina permit approval needed for the $650 million deepening of the Savannah River shipping channel.

The required state certification under the federal Clean Water Act has been the subject of a year of political debate and a lawsuit that has wound up before the South Carolina Supreme Court.

The corps says it wants the exemption to prevent what it calls “inappropriate delays” for the project.

The corps announced last week it has given its final approval to the deepening work, a priority for Georgia for 16 years so larger containerships can call at its port when the Panama Canal expansion is complete. The project would deepen the river channel and harbor entrance channel from its current 42 feet to 47 feet.

The letter seeking the exemption was written Friday to U.S. Sen. Barbara Boxer, D-Cal. and chairman of the Senate Committee on Environment and Public Works, by Jo-Ellen Darcy, the assistant secretary of the Army for Public Works. The AP acquired a copy Monday.

“Be advised that if Congress authorizes this project or next appropriates funds for construction” it would be providing an exemption, the letter states.

Last year, the board of the South Carolina Department of Health and Environmental Control granted the needed water quality certification, reversing its own staff which had said the dredging would harm endangered sturgeon in the river and fragile wetlands on the South Carolina shore.

The approval came shortly after Georgia Gov. Nathan Deal visited South Carolina to discuss the issue with Gov. Nikki Haley who appoints board members. Haley said Deal made a reasonable request and she did not pressure anyone for a specific outcome.

But environmental groups then sued, calling the certification illegal because the state’s Savannah River Maritime Commission has authority over dredging decisions.

The state Supreme Court heard arguments earlier this year and during the hearing Chief Justice Jean Toal told a DHEC attorney that the agency had disobeyed the law. The justices have yet to rule.

State lawmakers later also passed a law retroactively suspending DHEC’s ability to make dredging decisions concerning the river. While Haley vetoed it, she was overridden with the votes of all by one state lawmaker.

“Rather than accept this invitation by federal bureaucrats to disrespect South Carolina’s citizens, courts and environment, Congress should instead instruct the Corps of Engineers to assess whether expanding other regional harbors would save hundreds of millions in taxpayer money without devastating a major U.S. river,” said Blan Holman, an attorney for the Southern Environmental Law Center who represents environmental groups who challenged the DHEC approval.

It’s not the only lawsuit stemming from South Carolina review of the deepening project.

Environmental groups have also sued in federal court saying the project needs a South Carolina pollution permit because it will mean toxic cadmium will be dredged and deposited on the South Carolina shore.