A charity that once operated clinics on a barge known as the Floating Hospital agreed yesterday to pay $400,000 to settle claims it scammed millions in taxpayer funds by setting up dozens of clinics that billed Medicaid at exorbitant rates.

The Floating Hospital — which sold its boat after 9/11 and moved its offices from there to Queens — didn’t have to admit wrongdoing.

Papers filed in Manhattan federal court charge the hospital won approval for a Medicaid reimbursement rate of $218 per patient visit, the highest allowed by the state, based on the high costs of maintaining the vessel.

Between 1997 and 2004, it opened as many as 100 part-time clinics that offered physical and speech therapy to developmentally disabled patients, even though it didn’t provide those services at its main site, which is required by Medicaid rules.

Most clinics were run by vendors who got $85 per patient visit, with the hospital pocketing the rest of the $218 Medicaid payment, the papers say.