ALBANY — Negotiating his first state budget, Senate Majority Leader John Flanagan this month withstood pushback and showed he could marshal votes for a minimum-wage bill, but only after hours of discord that one Republican called a “brutal experience.”

In the end, Flanagan got his 30 Republican colleagues to stand together unanimously to pass a $156 billion budget that included Gov. Andrew M. Cuomo’s $15-per-hour minimum-wage proposal for downstate New York, even though several Republican senators vehemently and publicly opposed it.

Flanagan persevered, enduring a tense standoff right before the April 1 vote when the absence of state Sen. Tom Croci (R-Sayville) from the chamber sparked a closed-door meeting. Some said later that Flanagan keeping Republicans together as a bloc showed strength. But others clearly were chafed.

“He’s stronger, no question. He fought to keep the conference together,” one senator, who like others in the majority, spoke on the condition of anonymity about the closed-door talks, said Monday.

“I didn’t vote for him,” said the senator, referring to the vote last May that elevated Flanagan to majority leader, “but I was impressed and I told him so.”

But the praise wasn’t universal.

“This was not a case of ‘Hey, great for him. He got unanimity,’ ” said one Republican. “People did not like the way it was handled. How he got to unanimity damaged his leadership.”

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The senator quickly added the discord probably won’t foment a challenge to Flanagan’s post as leader or necessarily manifest itself in any way. But the senator said: “Republicans need time to heal.”

Flanagan, stoic after one of the longest sessions in recent Albany history, downplayed the tension.

“I think everybody had last-minute reservations,” Flanagan said. “Yeah, we got resistance because it’s real life.”

Cuomo, a Democrat, Flanagan (R-East Northport) and Assembly Speaker Carl Heastie (D-Bronx) negotiated right up to the state’s April 1 deadline for adopting a state budget, haggling intensely over not just the proposed minimum-wage increase but also school aid, cost shifts to New York City and public college tuition.

$15 per hour minimum wage priority for Cuomo

Cuomo made getting to a $15 per hour minimum wage his top priority. He sacrificed other proposals to get there and agreed to slow down his proposed implementation. On April 1, technically making the budget a day late, lawmakers agreed to raise the wage — currently at $9 per hour — in a series of steps to $15 per hour downstate. It will hit that mark on Long Island by Dec. 31, 2021.

Many of the 31 Senate Republicans wanted to delay the implementation further or oppose it altogether. Some Long Island senators wanted Nassau and Suffolk counties to be on the same rate schedule as upstate — where the wage will peak at $12.50 then be subject to a review that could eventually get it to $15. Some wanted to wait till after April 19, the date of crucial Senate election to fill the vacant seat of Flanagan’s predecessor, Dean Skelos of Rockville Centre, who was convicted last year on corruption charges.

Flanagan, after getting more school aid and a tax cut in the budget, basically said they couldn’t change the terms. It took a lot of “convincing, cajoling and arm-twisting” to keep the GOP vote together as a bloc, one said.

The drama played out behind closed doors and in the Capitol hallways before the vote was finally taken at 9:30 a.m. April 1.

On March 31, state Sen. John DeFrancisco (R-Syracuse) said he remained opposed to the wage hike, even as the midnight deadline neared for enacting an on-time budget.

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“I haven’t changed,” DeFrancisco said at 1 p.m. as he entered one of the many closed-door Republican conferences.

Upstate Republicans who had supported DeFrancisco in the skirmish to replace Skelos, including state Sen. Rich Funke (R-Rochester), grumbled to reporters that Cuomo’s minimum wage hike was too big and rose too fast for upstate employers and its shaky economic recovery.

Business lobbyists and conservative leaders urgently tried to stop the wage hike. Millionaire Buffalo developer Carl Paladino, the GOP’s 2010 gubernatorial candidate, on March 31 sent a stinging email to conservative Republicans and reporters in which he accused Flanagan and his Senate Republican followers of being RINOs — “Republicans in name only” — over the minimum wage deal.

Playing his own card, Cuomo held a formal news conference late the same day — notably without legislative leaders — to announce negotiations were done and a budget deal was struck even as Republicans continued to argue.

Then Cuomo and the legislative leaders agreed to tuck the minimum-wage initiative into the voluminous budget bill that included the boost in school aid, which was the top priority of Senate Republicans. That forced Senate Republicans to accept the whole bill — including the wage hike — or reject it.

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And there was the threat of deploying a wage board.

“We felt we needed to mitigate it,” said one Republican senator.

Flanagan’s style differs from Skelos’

Flanagan then had to wrangle votes to present a unanimous front to avoid relying on any Democratic votes, which Republicans senators said could show weakness or result in a debt to Democrats for favors down the road.

In doing so, Flanagan displayed a different style than Skelos. It was more open and direct, but some could have seen it as bullying, sources said. That approach can take more time to arrive at a consensus and be a bit more frustrating but is welcome, one senator said.

Yet as late as April 1 at dawn, after a 17-hour session of passing budget bills, Flanagan still faced internal resistance.

Croci balked, as he was not in his seat when the bill was called to the floor. Lacking Croci’s vote, that forced Flanagan to adjourn the marathon session to convene yet another Republican skull session to discuss the vote behind closed doors.

Flanagan and others believed the “good outweighed the bad,” DeFrancisco said, highlighting school aid and tax cuts. Republicans also secured more aid for charter schools as part of the final haggling. Some argued that opposing minimum wage would hurt Republicans in the fall elections.

Afterward, Croci, like all the Republicans, voted “yes.” He declined to talk to reporters.

In the end, the internal push for unanimity won out.

“We felt it was important for us to remain a team, in the good and the bad, because we are in a situation that we believe it is important to stay together in view of the fact that we would like to have a Republican majority next year,” DeFrancisco said. Republicans hold just 31 of the 63 seats but govern with the alliance of six breakaway Democrats.