In making his announcement in August, Mr. Cuomo, a Democrat, had sought to frame the subsidies as a way to help achieve renewable energy goals as part of his so-called Clean Energy Standard, which requires half of the state’s electricity to be produced by sources like wind and solar by 2030.

In its order, the Public Service Commission pointed out that the state’s upstate nuclear plants “avoid the emission of over 15 million tons of carbon dioxide per year,” and that losing their production “would undoubtedly result in significantly increased air emissions due to heavier reliance on existing fossil-fueled plants or the construction of new gas plants to replace the supplanted energy.”

On Wednesday, Ms. Zibelman characterized the lawsuit as “frivolous,” saying in a statement that it was “right out of the fossil fuel industry’s playbook to deny and thwart actions to combat climate change.”

“The Supreme Court has repeatedly upheld the rights of states to protect their environment for the welfare of citizens,” she added. The commission also disputes the cost estimates made in the suit, saying it believes the financial impact would be “less than $2 per month for a typical residential customer.”

The four plants involved in the subsidy plan include two at the Nine Mile Nuclear Station in Scriba, N.Y., and the Robert Emmett Ginna Plant, east of Rochester, as well as the James A. Fitzpatrick Nuclear Power Plant, also in Scriba. One of the two Nine Mile plants is financially feasible, according to the suit.