U.S. District Judge Amy Totenberg granted a request from a group of health systems to delay the policy while they appeal her earlier decision that HHS could move forward with the plans. HHS was set to start implementing the new liver distribution system May 14.
"The court again finds itself thrust into maelstrom of this preliminary issue prior to the court of appeals having a chance to weigh in on the matter," she wrote in Wednesday's ruling.
In light of the new order the United Network for Organ Sharing, which oversees organ distribution in the U.S., asked for clarification from the judge as "the policy has already been implemented."
The group said that the new liver matching system is underway.
"In the meantime, (organ procurement organizations) and transplant centers should follow the match runs that UNet generates," UNOS said. "If we make changes to UNet, we will notify the community."
Initially the policy, adopted last December, was supposed to go into effect April 30. A coalition of health systems and patients in states that liked the longstanding, geography-based allocation system sued, the department agreed to stall its implementation until May 14 as Judge Totenberg reviewed the case.
The judge noted that she had very little time to untangle all the complicated medical and legal issues of the liver allocation system. She also expressed reservations about the government's decision to proceed with the new policy.
The injunction pending the appeal essentially freezes the status quo and "minimizes major disruption in the liver transplant medical field," she wrote.
Emory University Hospital and Piedmont Hospital in Georgia, the University of Michigan, and the University of Kansas Hospital Authority are part of the health system coalition that has sued to block the change. Patients who expect to lose their place in the line for a liver transplant were also plaintiffs in the lawsuit.
Hospitals with transplant centers are set to lose a chunk of lucrative business under the revised policy.
In Congress, Sens. Roy Blunt (R-Mo.) and Jerry Moran (R-Kan.) have been putting pressure on the Trump administration over the policy that has become sharply political because it pits regions of the country against one another.
Late Tuesday, Blunt called the proposed changes "simply wrong" in a statement.
"It will lead to higher costs and fewer transplants in our region, all while providing no improvement in patient outcomes," Blunt said. "I will continue challenging this unfair action and hope the courts will put a permanent stop to it."
The new policy was approved last December by UNOS, a stakeholder board tasked by HHS' Health Resources and Services Administration to oversee the national organ allocation system.
UNOS has acknowledged the divisiveness of the issue, but stands firmly behind the change. In a statement on Tuesday the group issued a statement welcoming Totenberg's initial ruling.
"The new liver allocation policy will save lives," UNOS said.