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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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