Two years ago, the state said it might not pay for traumatic brain injury therapy any more. A revolt occurred.

In a compromise, Maine kept up Medicaid reimbursements, but at lower rates that kicked in last December.

In seven months’ time, Goodwill Industries, which operates two outpatient treatment centers for neural rehab in Lewiston and Portland, lost $500,000.

The nonprofit trimmed staff, cut expenses. This fiscal year, it was going to happen again: $500,000 less than it costs to operate.

Meanwhile, similar programs offered by other agencies closed in Brewer, Brunswick and South Portland. Goodwill and other providers complained. The state responded Wednesday with an emergency order for more money.

Brenda Harvey, with the Department of Health and Human Services, said the temporary rule change will boost reimbursement rates.

For instance, the state will pay $100 an hour versus $80 for therapy to help someone just out of the hospital.

“We are so relieved,” said Marsha Martino, director of neural rehabilitation services for Goodwill. “Our rates didn’t even cover our direct costs. This rate allows us to break even.”

Goodwill spokeswoman Jean Salce said WestSide in Lewiston and BaySide in Portland each serve about 100 to 150 people a year with acquired brain injury – they’ve had an accident, fallen, gotten cancer or had a stroke.

Most of the funding for that sort of program relies on Medicaid.

“There were a few months we were wondering if we were going to have to close one of our programs. We couldn’t have gone on realizing these big losses,” she said.