Senate Majority Leader John Flanagan Friday rejected key proposals in Gov. Andrew M. Cuomo’s State of the State addresses this week, saying free college tuition for low- and middle- income families may cost too much and closing the Indian Point nuclear plant would result in job losses and higher energy costs.

In his most extensive comments to date about Cuomo’s proposals, which are likely to be included in the 2017-18 budget, Flanagan told business and political leaders in Woodbury that Senate Republicans would resist efforts by Cuomo to fund his agenda through an extension or expansion of the “millionaires tax,” which is set to expire at year’s end.

“My biggest concern is not the value or the quality of these programs but how do we pay for them?” Flanagan said at a breakfast hosted by the Long Island Association, the region’s largest business group. “Every time people have to dig deeper in their pockets, that creates situations that we don’t necessarily want to have.”

Cuomo spokesman Rich Azzopardi said Flanagan “wants to cut taxes on millionaires and deprive middle class families of college tuition assistance. We think he’s wrong on both counts.”

In six regional State of the State addresses, Cuomo called for spending $163 million to provide free tuition for families earning less than $125,000 at State University of New York or City University of New York two- and four-year schools.

Cuomo also announced plans to close Indian Point in Westchester County by 2021, calling it a “ticking time bomb.”

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Flanagan (R-East Northport) called the free tuition proposal “laudable.” But he questioned its cost and said it would “exacerbate” financial problems of private universities.

Lt. Gov Kathy Hochul, who also spoke at the event, defended the plan.

“If you think it’s too expensive, consider the cost of not educating these individuals,” she said. “Consider the social costs of people who fall through the cracks.”

Flanagan said the decision to close Indian Point was made without input from Westchester County political leaders and would cost the state jobs and result in higher energy costs.

“I don’t know that it’s a good idea,” he said of the proposal to close the plant. Flanagan said the ramifications “will be felt across the state.”

The governor’s office estimates that electric bills would increase by about $3 a month due to the closure. The administration says the state will invest in wind farms and other renewable energy sources to replace the plant’s capacity.

Flanagan also called for Cuomo’s budget to include a property tax cap for New York City — matching a 2-percent cap in place for municipalities across the state — and to impose a similar cap on all state spending.

State budgets have stayed under a 2 percent cap in recent years but the policy is not law.

In an interview Friday, Flanagan also confirmed a Newsday report that he is considering a run for governor in 2018.

Flanagan called the gubernatorial post “the best public service job in the state” and said he has given some thought to seeking the office. But for now, Flanagan said he “is concentrating on the work of the Senate.”