The plan involves idling three of the five boilers at the massive Four Corners Power plant and adding new emissions-control gear to the other two.
Hearings will be conducted in March and other public comments will be accepted by the EPA until May 1.
EPA officials in San Francisco said in a written statement the proposal, which was originally made by one of the plant's owners, Arizona Public Service, would take older, less-efficient boilers off line. The move would cut nitrous oxide emissions by 87 percent and also reduce other emissions, such as mercury.
The agency had earlier come up with a plan to reduce emissions 80 percent. "The new proposal controls emissions better, while costing less and preserving jobs," said Jared Blumenfeld, the EPA's regional administrator for the Pacific Southwest. "This plant is the nation's largest source of nitrogen oxides."
Blumenfeld said a side benefit would be better visibility at national parks and wilderness in the area.
Four Corners is on Navajo land and burns low-sulfur coal that is turned into electricity consumed in New Mexico, Arizona, Texas and Southern California. The plant's current capacity is 2,040 megawatts. APS has said shutting down the three older boilers would reduce capacity by about 560 megawatts.