At issue is the constitutionality of the law signed by US President Barack Obama, and how it legally obligates individuals to purchase healthcare coverage.
Judge Roger Vinson of the northern district court of Florida said that the lawsuit brought by 16 state attorneys-general, four state governors, a mutual benefit corporation and two private individuals could go ahead on two counts.
In one of those counts the states objected to the constitutionality of "fundamental changes in the nature and scope of the Medicaid program" that resulted from healthcare legislation.
In the other they challenged the legality of the obligation of individuals to purchase healthcare coverage.
The judge dismissed four other counts.
Obama signed the healthcare reform bill into law on March 23. The same day, the attorneys-general of 13 states, led by Florida attorney-general Bob McCollum, filed suit in the northern Florida district court against the law.
They were joined three months later by three more state attorneys-general, the governors of Arizona, Georgia, Mississippi and Nevada; California nonprofit mutual benefit corporation the National Federation of Independent Business; and two individual complainants.
On Thursday, McCollum called the judge's decision "a victory for the states, small businesses and the American people.
"Congress has no constitutional authority to force the individual mandate and its penalty on Americans who cannot afford or do not wish to have health insurance," he said in a statement.
"Furthermore, our system of federalism under the US constitution ensures that federal government cannot bully the states by forcing us into a no-win decision," he added.
"Obamacare imposes a massive expansion of the Medicaid entitlement program on the states - a financial burden that states and taxpayers do not want and cannot afford."
The decision means the summary judgment hearing for the case will go ahead on December 16, he said.
