A federal judge in Boston has ordered a temporary pause nationwide on plans by the National Institutes of Health (NIH) to substantially reduce “indirect” research payments to universities, medical centers and other recipients. 

U.S. District Court Judge Angel Kelley of the U.S. District Court for the District of Massachusetts granted the temporary restraining order in response to a lawsuit filed by associations representing teaching hospitals, public health and pharmacy schools and Boston and New York-area hospitals. 

The nationwide pause, issued late Monday, came after Kelley granted another restraining order in response to a lawsuit from 22 state attorneys general. But that restraining order only applied to the states that sued, meaning the rate cut was still in effect in the rest of the country. 

The pause will remain in place until lifted by the court. 

Late Friday, NIH said it would set a 15 percent cap on payments for indirect costs which are administrative and facility costs linked to research, such as utilities and support staff. The cap was in lieu of a separately negotiated rate for indirect costs in every grant. 

Scientists, universities and lawmakers raised immediate alarms. 

Republican Sens. Susan Collins (Maine) and Katie Britt (Ala.) expressed concern over the funding cuts on Monday, with Collins saying she opposes the “poorly conceived directive.” 

Britt said in an interview with Al.com said that the funding cuts should be carried out with a targeted approach in order to “not hinder lifesaving, groundbreaking research at high-achieving institutions like those in Alabama.”