A federal judge late on Wednesday cleared the way for Steward Health Care to close two Massachusetts hospitals, while the fate of the company’s other hospitals remains unsettled, and Steward runs critically low on cash.

Judge Christopher Lopez of the US Bankruptcy Court in Houston called the decision "painful” while ruling that Steward met the legal standard for shutting down Carney Hospital in Dorchester and Nashoba Valley Medical Center in Ayer. “It’s affecting the lives of people who are in there right now,” he said. “The importance of every individual who’s in there weighs on me. Steward is running out of money to operate and continues to mount financial losses.”

“To keep those hospitals open, based upon the evidence before me, threatens the entire hospital system in Massachusetts,” the judge said, speaking haltingly, near the end of the two-and-a-half hour hearing. His ruling came despite a dire warning from the Massachusetts Nurses Association that people could die if they have to travel farther and wait longer for care.

Hugh McDonald, a lawyer representing Massachusetts, said state officials are disappointed about the closures but will work with Steward officials to relocate the patients at Carney and Nashoba Valley. “We have seen this coming,” he said. “We have prepared for this. We are trying our very best to make sure, through cooperation, we are going to get these patients into safe facilities.”

The bankruptcy judge also approved a request from Steward to reject a lease agreement that Steward and Massachusetts officials say has stalled the process of transferring Steward hospitals to new owners. Steward’s lawyers said the company received bids from “high-quality” operators for most of the Massachusetts hospitals, but none of the bidders want to assume expensive lease payments.

Steward sold its real estate to another company, Medical Properties Trust, in 2016. The Massachusetts properties now are jointly owned by MPT and another firm, Macquarie Asset Management. Yet another company in the mix is Apollo Global Management, a lender to MPT and Macquarie.

“It’s an immensely complex negotiation,” said Ray Schrock, a lawyer representing Steward. He urged representatives from these firms to get together in New York this week to resolve the real estate issues. “We will stay there as long as we need to. People should bring clothes, because we have to get this done,” Schrock said. “We’re already in overtime, effectively.”

Massachusetts officials have admonished the real estate firms for blocking deals on Steward’s hospitals by trying to extract as much money as they can from the process. “The infighting, this brinkmanship … has led us to the place where we are today. The commonwealth is losing its patience,” said McDonald, the state’s lawyer.

Still unresolved is the issue of funding to keep Steward’s hospitals afloat through the next month. Massachusetts officials have offered $30 million in advance Medicaid payments to help the hospitals continue operating — but only if Steward signs sales agreements for its remaining five hospitals.

Those agreements were supposed to be finalized by the end of July, but Massachusetts officials decided to give Steward another week to finish the deals.

“It’s clear through the bankruptcy process that Steward’s decision to sell properties to Medical Properties Trust has jeopardized community care,” said Tim Foley, executive vice president of 1199SEIU, a labor union representing 5,000 workers across Steward hospitals in Massachusetts. “We need to ensure that these hospitals are transitioned, as many as we can, to not-for-profit owners who are going to put patients first.”

Labor leaders and elected officials have been protesting the planned hospital closures in Ayer and Dorchester — one in a rural part of the state, the other in an urban area. Some health care leaders have warned that the closures will exacerbate health disparities.

Steward first announced the closures less than a week ago and plans to shutter the hospitals by Aug. 31, even though state law requires 120 days’ notice.

Eliza Williamson, executive director of the National Alliance on Mental Illness of Massachusetts, said Carney and Nashoba Valley together have 70 licensed psychiatric beds. She said the loss of these beds is devastating for the state and expects it will be very difficult to find places to transfer patients.

“I don’t think we can underestimate the crisis that this could cause,” Williamson said. “Even if there was a place for these patients to go, transfers would be deeply challenging. But there is nowhere for people to go."

According to Massachusetts officials, a total of 45 patients were at Carney Hospital on Wednesday, while Nashoba Valley had just 21 patients.