Clement argued that the government had gone too far in asking the states to add significant administrative expenses and force them to eventually cover more citizens through Medicaid.
But the Court ruled that the Medicaid expansion is constitutional.
The Department of Justice issued a statement following the opinion, saying it "strongly" disagreed with the decision and that it is "considering the next appropriate steps."
Supporters of the law joined in the criticism.
"The 11th Circuit majority ignored the text and history of the Constitution, centuries of Supreme Court precedent, and the basic reality of our health care system," said Elizabeth Wydra, chief counsel of the Constitutional Accountability Center.
But Georgetown law professor Randy Barnett ,who represented the States in the case, issued a statement hoping the Supreme Court would take up the issue.
"Now that judges appointed by both Democratic and Republican presidents have found the individual insurance mandate to be unconstitutional, the nation's interest requires the Supreme Court to hear this case next term. Only then would the uncertainty inflicted upon the national economy by this unprecedented and unconstitutional law be lifted. "