ALBANY — A congestion pricing program for New York City would provide $1 billion for the Long Island Rail Road under an agreement struck Thursday in state budget negotiations, according to an official familiar with the deal.

Gov. Andrew M. Cuomo's congestion pricing plan would raise billions of dollars in tolls charged to motorists driving into Manhattan below 60th Street. The aim is to reduce traffic congestion while raising money to fix New York City’s subways and commuter rails.

The Long Island Rail Road would get 10 percent of the revenue, the Metro North commuter rail system would get 10 percent, and NYC Transit, which includes subways and buses, would get 80 percent of revenue, according to the official, who spoke on the condition of anonymity because the budget deal hadn't yet been announced.

The projected revenue and the tolls weren't released.

Earlier Thursday, Assembly Speaker Carl Heastie said discussions were down to deciding how to make sure commuters aren’t charged double for commuting along the Robert F. Kennedy Bridge and other bridges into the congestion pricing zone. The balancing act, he said, was to not to exempt so many commuters that the plan becomes underfunded.

Reached on Thursday night, MTA Board Member Mitchell Pally of Stony Brook said the money could be used to modernize the LIRR's antiquated signal system, expedite planned capacity upgrades at Jamaica station, and even help advance long-discussed plans to electrify the railroad’s Main Line as far as Yaphank.

“The Long Island delegation made it clear that their support was dependent upon it,” Pally said, referring to the funds.

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Additional deals were starting to emerge for the state budget that is due by Sunday night at midnight. Voluminous budget bills were expected to be agreed to overnight, according to Heastie (D-Bronx) and Senate Majority Leader Andrea Stewart-Cousins (D-Yonkers).

A modest increase in school aid and a congestion pricing program after a decade of trying were expected to be part of an on-time state budget, legislative leaders said Thursday.

But Heastie warned a deficit of more than $3 billion, declining tax revenue and forecast of a recession that could weaken state resources within two years is resulting in a budget that will disappoint some of Albany’s strongest lobbies.

“We have difficult financial times; we are trying to at least reach last year’s ‘foundation aid’ number,” Heastie told Newsday.

The leaders were near agreement on increasing foundation aid for schools by about $620 million in the 2019-20 budget. Foundation aid is the primary school aid fund.

Overall, Cuomo had proposed a $956 million increase in school aid, to a proposed $27.6 billion.

Teachers unions and school funding advocates, however, had said at least twice the amount is needed.

“We don’t have the revenue,” Heastie said.

Legislators had said the school aid increase was often tied to Cuomo’s must-have proposal of making the state property tax cap permanent. The cap created by Cuomo requires school districts and local governments to keep the increase in their tax levies to under 2 percent, or to have a public vote that scores a supermajority to exceed it.

The Senate’s Democratic majority has supported making the cap permanent, but the Assembly’s Democratic majority had wanted changes. School districts had said the cap has cut schools to the bone and hurt programs while increasing the size of classrooms.

Cuomo, however, has made the issue one of his requirements for agreement on a budget and noted that Long Island and Westchester have among the highest property taxes in the country. The Democrat’s answers in recent news conferences to a proposed weakening of the cap was: “No. No. No. No.”

Heastie, however, said Thursday afternoon that making the tax cap permanent is “still under discussion.”

The cap doesn’t expire until 2020.

With Alfonso A. Castillo