Manchin on Wednesday denied any connection between the federal lawsuit and his campaign to finish the remaining two years of the late U.S. Sen. Robert C. Byrd's term.
The Democratic governor said the suit was already being prepared amid rising concern that U.S. coal policies harm West Virginia's mining economy months before Byrd died in June. The state hired a Charleston law firm to prepare for a suit and state Environmental Protection Secretary Randy Huffman said in June that litigation was imminent.
"Over the past year and a half, we have been fighting President Obama's administration's attempts to destroy the coal mining industry," Manchin said at a news conference Wednesday.
GOP rival John Raese, a businessman with a shot at a Senate seat the Republicans once considered unwinnable, characterized the suit as flip-flopping by Manchin.
The race is to replace Byrd, a Democrat who served more than a half-century on Capitol Hill.
West Virginia is heavily Democratic, but President Barack Obama didn't carry the state in 2008 and stricter regulation of the mining industry has not improved the president's standing in the No. 2 coal producing state.
Manchin can count on support from organized labor, the West Virginia Coal Association and the U.S. Chamber of Commerce.
But the National Republican Senatorial Committee is spending $1.3 million on ads attacking Manchin. And state Republicans are preparing an effort to plant 2,500 yard signs across West Virginia reading: "Obama Says 'Vote Democrat.'"
The lawsuit filed by state environmental regulators in U.S. District Court in Charleston names the federal Environmental Protection Agency and its administrator, Lisa Jackson, as defendants.
It targets EPA policies adopted since Obama took office that are designed to limit the practice of burying streams under excess rock. Critics say that practice destroys the environment; the mining industry defends it as an efficient way to produce cheap power and employ thousands in well-paying jobs.
Since Obama took office, the flow of water quality permits for Appalachian mines has slowed to a trickle.
"People's jobs are in jeopardy," Manchin said. "We've got too much of our economy and too many jobs and people's families at stake."
However, Raese's campaign said the suit represented another example of the governor trying to distance himself from Obama.
"He proceeded to take absolutely no legal action against the EPA's regulations until he dropped behind in the polls just weeks before the election," spokesman Kevin McLaughlin insisted in an e-mail.