"When this was rushed through a few years ago, it was done with a party-line vote, 2,700-page bill. I think the American people made it very clear, they don't like this law and there is a much better way," he said on MSNBC's "Morning Joe" on Thursday.
Thune said he believes people are most concerned about the affordability of healthcare in the United States and Obama's proposal fails to properly address those concerns.
"It is raising costs, it is hurting jobs out there, because small businesses are dealing with these mandates and the uncertainty associated with the bill and as a consequence we're not seeing people get back to work," he added.
Thune also addressed reports that some senators might be working on a plan to deal with tax cuts, entitlements and sequestration before the November election.
"There are people on both sides … who would love to see this addressed before the election for a lot of reasons, and not the least of which is, I think this is hurting the economy now," he said.
Thune told MSNBC that although the House is scheduled to vote on extending all of the Bush-era tax rates next month, bipartisan support in the Senate will depend on the president's support for a plan.
"I don't think the Democrats in the Senate are going to do anything unless the president is on board with that," Thune said.