A 14-year battle to renegotiate the original agreement for the Ranger Uranium Mine - surrounded by Kakadu National Park - has been settled.

The new agreement will see Energy Resources of Australia pay increased mining royalties and form a sustainability trust for the Mirrar people.

The executive officer of the Gundjeihmi Aboriginal Corporation, Justin O'Brien, says it is a new era of good relations with ERA.

However, he says the Mirrar have missed out on years of appropriate compensation.

"It's a bitter sweet moment for the traditional owners," he said.

"It has taken so long to get to this point that the increased benefits that will come to the Traditional Owners are significantly reduced."

Energy Resources of Australia's chief executive Rob Atkinson says the new agreement is a milestone for all involved.

"What I think today does is help to draw somewhat of a line across what's happened in the past, and allows us all to look more into the future," he said.

Senior traditional owner Yvonne Margarula says the new deal is much fairer.

"Today we happy all Mirrar, but a long time with my father," she said.

"He didn't agree with that mine because they pushed it to go through."

The renegotiated agreement does not apply to ERA's proposed underground mine at Ranger.