Activist Robert F. Kennedy Jr. is praising the Obama administration for moving to stop “the greatest environmental tragedy ever to befall our nation” while the coal industry says the administration has put tens of thousands of jobs at risk throughout Appalachia. But federal officials say they have done neither.

Still, it was easy to see why people might be confused. The uproar sprang from an announcement Tuesday that the Environmental Protection Agency had sent letters to the U.S. Army Corps of Engineers recommending denial of at least two permits for mountaintop mining because of the potential environmental harm from dumping associated debris in nearby riverbeds. Sounds pretty straightforward. But then the EPA made another, after-hours announcement saying that it “is not halting, holding or placing a moratorium” on any applications for the mining industry to dispose of its overburden in waterway areas or streams. The final decision is actually up to the Corps of Engineers.

The EPA said further that it “will take a close look at other permits” — and in this, at least, is signaling a major shift from the Bush administration’s mountaintop mining policy.

In mountaintop mining, miners use explosives to blast away summits and expose seams of coal. Huge machines then push the debris into the valley below. The EPA estimated that mountaintop removal has filled in some 1,200 miles of streams and completely destroyed another 700 miles worth of waterways.

The two permits that the EPA addressed this week involved mining operations that the agency said would have caused permanent damage to 3.5 miles of streams in Kentucky and 2.5 miles of headwater streams in West Virginia. Although some of the channels are dry part of the year, the EPA said they were “essential to the overall health” of the waterways downstream.

But in its late press release the EPA signaled that the majority of mining permits would not pose the same issues. “We fully anticipate that the bulk of these pending permit applications will not raise environmental concerns,” the agency said.

Carol Raulston, spokeswoman for the National Mining Association, said, “We certainly hope that that characterization is true.” But she said in her view this morning’s Washington Post op-ed by RFK Jr. suggested he knew “what was in the works” before the mining industry — which learned about the move when it began receiving calls from reporters yesterday afternoon. In the op-ed Kennedy calls on the administration to “enlarge its moratorium” by suspending a dozen already-issued permits.

Mining operations, Raulston said, typically need to apply for a series of permits to discharge into waterways so even ongoing operations are affected by EPA’s notice. That’s why Raulston’s boss, NMA president Hal Quinn took aim at the agency in a prepared statement: “Jeopardizing coal mining activity throughout Appalachia will put more than 77,000 high-wage mining jobs at risk at a time when our nation is already battered by a deepening recession.” NMA’s mining employment numbers show 63,825 miners in the Eastern region, of whom 21,600 work on surface mines, which include mountaintop mining sites.

“This has been such a surprising course of action,” said Raulston, who added that the Obama administration “has been very positive about coal and the role coal can play in meeting our energy security needs, and also providing money for clean coal technology.”

But if you clear away the dust from the original blast of news from the EPA, no one is ready to declare victory. Sierra Club spokesperson Josh Dorner told PaperTrail, “I think [Obama] is definitely moving in the direction of ending mountaintop mining, but this is just the first step.”

Aaron Mehta contributed to this post.