More than two-thirds of Connecticut hospitals will face Medicare penalties for lagging clinical-care measures in the fiscal year that began Oct. 1, with smaller hospitals including Johnson Memorial, Windham and New Milford losing the highest percentage of reimbursement.

The penalties, under a federal program known as Value-Based Purchasing, average .26 percent nationally, with Connecticut’s hospitals losing an average of .23 percent, according to federal data compiled by Kaiser Health News. None of the state’s hospitals will lose the maximum possible penalty, 1.25 percent of funding, federal data shows.

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