THE LEGISLATURE adjourned early Thursday morning with no agreement between the two branches on an omnibus close-out spending bill that included $250 million to keep the state’s emergency shelter system afloat.

The two branches individually debated and approved other pieces of legislation on Wednesday – a pharmaceutical bill in the Senate and a long-term care bill in the House – but the leaders of the two branches were unable to come to agreement on the one bill that many felt needed to get done before the Legislature recessed for its holiday break.

The failure to reach agreement on the bill means final action could be put off until at least early January unless the branches can somehow pass it during informal sessions, when the objection of one member can stop it from being voted on. House and Senate leaders said they hoped to get the bill approved before January.

Even with the Healey administration’s decision to cap the number of families in the emergency shelter system, the program’s funding is expected to run out sometime in January. The $250 million was needed to keep the system operating.

Sen. Michael Rodrigues of Westport, the chair of the Senate Ways and Means Committee, had confidently predicted he would get a deal done before the Legislature recessed, but after negotiating all day long with his counterpart in the House, Rep. Aaron Michlewitz of Boston, nothing materialized.

“We’re very disappointed,” Rodrigues said. “Our goal was to get it done tonight, but we’ll start in again tomorrow.”

The money wasn’t the sticking point. Both branches were willing to appropriate another $250 million for the shelter system, on top of the $325 million appropriated in the initial state budget, but they differed on how the money should be spent.

The House was very prescriptive in the bill it passed last week, designating how the $250 million should be spent and requiring the establishment of overflow sites within 30 days to care for families expected to end up on Gov. Maura Healey’s waitlist for shelter spots. The House also gave the Healey administration 30 days to get an overflow site up and running or see its 7,500-family cap revoked.

The Senate, by contrast, gave authority to the Healey administration to spend the money as it saw fit. Senators said it made more sense for the governor, whose administration is overseeing the shelter system, to distribute the funding as needed, although some in the Senate said they did not want to get sucked into micromanaging a situation that appears to be spiraling out of control.

House Speaker Ronald Mariano said he wanted to see a real plan for dealing with those families who are homeless and waitlisted for shelter. Michlewitz agreed. “We want to prevent people from sleeping in the streets or sleeping in our airports or our train stations or our emergency rooms,” he said.

The spending bill included a hodge-podge of other appropriations to close the books on fiscal 2023, which ended more than four months ago, and a series of one-off initiatives, including a provision that would have given life to efforts to build a professional soccer stadium in Everett and another measure allowing the company building a Massachusetts-financed transmission line from Quebec into New England to secure additional funding because of delays beyond its control in building the line.

It was all part of a strange night on Beacon Hill. Normally when the two branches can’t agree on a bill, the two chambers each appoint three-member conference committees to find common ground. Last night Rodrigues and Michlewitz tried to handle the negotiations themselves.

Shortly before midnight, when the Legislature was scheduled to recess for the holiday break, the Senate suspended its rules and agreed to stay in session beyond midnight. The House took no action to extend its session but members remained on standby nonetheless.

At 12:30 a.m., Michlewitz came in to the chamber, chatted with a number of House members, and then left. Shortly afterward, the House appointed a conference committee and recessed. The Senate followed suit shortly after. No one publicly explained what went wrong to the members of the House and Senate.