The lawsuit, filed last week in federal court, alleges that the U.S. Department of Health and Human Services is trying to coerce Florida into expanding Medicaid by threatening to end a $2.2 billion program that helps hospitals pay for uncompensated care.
The Republican governor now wants a court-ordered injunction to stop federal health officials from tying the two programs.
"Unless this unconstitutional coercion is redressed, it will have immediate and devastating consequences for Florida, its healthcare providers, and its residents," Scott's attorneys wrote Thursday.
HHS has long maintained that Medicaid expansion is a state decision.
The agency says it is willing to work with Florida to address uncompensated care, regardless of the state's Medicaid expansion status. But top federal health officials have also said they want Florida to expand health insurance coverage, which would reduce the need for the so-called Low Income Pool, or LIP.
Florida has yet to learn if LIP will be renewed next year. The program is scheduled to end on June 30 unless the federal government approves a proposed successor program.
If no deal is reached, Jackson Health System in Miami and Tampa General could face $200 million and $86 million in cuts, respectively.
Scott made an appeal for the money to HHS Secretary Sylvia Burwell on Wednesday, but left Washington empty handed. The agency later published a statement saying the Florida proposal fell short of the federal guidelines for funding uncompensated care pools, and that Florida seemed to be asking for too much money.