U.S. District Judge Roger Vinson had said at a hearing last month that he would block efforts by the Justice Department to dismiss the lawsuit, led by Florida and 19 other states.
"In this order, I have not attempted to determine whether the line between constitutional and extraconstitutional government has been crossed," Vinson, of the U.S. District Court for the Northern District of Florida, wrote in his ruling.
"I am only saying that ... the plaintiffs have at least stated a plausible claim that the line has been crossed," Vinson said.
Opponents of Obama's overhaul of the $2.5 trillion U.S. healthcare system have said it violates the Constitution by imposing what they consider unlawful taxes and requiring citizens to obtain healthcare coverage, among other issues.
The suit was originally filed in March by mostly Republican state attorneys general.
The ruling allowing the case to proceed was a setback for Obama, who has made healthcare reform a cornerstone of his agenda and who is struggling to fight off a strong Republican challenge in November 2 mid-term Congressional elections.
Vinson dismissed four of six claims the states brought against the healthcare law but said he saw grounds to proceed on two counts, including one relating to the way critics say it would force huge new spending by state governments.
On the issue of the so-called "individual mandate," the law's provision that all Americans obtain healthcare insurance, Vinson said the plaintiffs had "most definitely stated a plausible claim" for their objections.
"The power that the individual mandate seeks to harness is simply without prior precedent," he said.
The White House said the government expects to prevail.
"We saw this with the Social Security Act, the Civil Rights Act, and the Voting Rights Act -- constitutional challenges were brought to all three of these monumental pieces of legislation, and all of those challenges failed," presidential adviser Stephanie Cutter wrote in a blog post.
"VICTORY FOR STATES"
Vinson said the case would continue as scheduled. He had previously set a hearing for December 16.
"This ruling is a victory for the states, small businesses and the American people," Florida Attorney General Bill McCollum said.