"I think the Massachusetts proposal, which is frankly the beta version of what Obamacare is, is not working," he said. "There has be to be a fundamental restructuring of how we think of the delivery of health care. Unless that's achieved it almost doesn't matter where the focus of authority is."
Health care is also likely to come up in deficit talks as the new Congress looks at new ways to manage the country's massive budget deficit.
House Republicans are already discussing ways to defund parts of the contentious law.
"The real political dynamite will be funding for implementing reform. The stopgap funding bill that keeps the government going until March has already cut funding for the roll-out," said Robert I. Field, professor of health management and policy at Drexel University school of public health. "Spending bills originate in House, which will be Republican-controlled. That will give them a perfect grandstand for showcasing their opposition to reform."
As senators and members of the House -- who are sure to take a vote on repealing the law -- work out new plans, the administration is rolling out the law as planned, including funnelling millions of dollars to states to modernize their systems.
Speaker Nancy Pelosi vowed in a statement Thursday that "Democrats will fight to preserve these gains for the American people in the months and years to come," signaling the start of what could be a tough battle for Democrats ahead.
The challenges they face ahead are numerous. Some states have refused to move forward with the law or, like Arizona, are refusing to accept federal grants for expanding Medicaid.
Lawmakers are threatening to repeal key parts of the law that could derail it altogether. The lawsuit pending in Florida currently specifically targets the constitutionality of the provision that requires all Americans to carry health insurance.
The individual mandate is the cornerstone of the new health care law, and overturning that, insurance companies say, would be drastic to their bottom lines since they need that assurance to comply with new restrictions that have been placed on them.
"Without the individual insurance mandate, most of the rest of the law -- no exclusion for pre-existing conditions, no lifetime ceiling, etc. -- cannot function and at that point will have to be repealed," said Daniel S. Blumenthal, associate dean for community health at Morehouse School of Medicine.
ABC News' Kim Carollo contributed to this report.