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WASHINGTON — The Department of Health and Human Services will get to decide how to compensate hospitals for years of underpayments related to a federal drug discount program, a federal court decided Tuesday.

The decision is the latest installment in a legal dispute between hospitals that get discounted drugs through the 340B program and the federal government over Medicare payment formulas. The repayments HHS owes hospitals total more than $1 billion, and hospitals had hoped the court would force the government to pay them back immediately.

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“We urge HHS to honor the plain language of the ruling, which calls on the department to ‘act promptly’ to repay the more than five years of funding lost to these cuts,” said Bruce Siegel, president and CEO of the safety-net hospital lobby America’s Essential Hospitals.

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