Senate Parliamentarian Alan Frumin upheld two Republican challenges under budget reconciliation rules, Senate Democratic aides said, requiring another vote by the House just days after it passed the package during a contentious debate on Sunday.
The challenges involve the package's revamp of the student loan program, said Jim Manley, a spokesman for Senate Democratic leader Harry Reid. Under reconciliation rules, each provision in the package must have a budgetary impact.
The decision came as the US Senate met in a middle-of-the-night session to try to finish the bill, which would put the finishing touches on the sweeping health care overhaul signed into law by President Barack Obama on Tuesday.
The decision set up another potentially difficult vote in the House, which narrowly passed the $940 billion overhaul on Sunday along with the companion bill of final changes after a sometimes bitter yearlong political struggle.
Republicans had met with the parliamentarian through the night on Wednesday to find language that could be challenged under reconciliation rules. Those rules were being used because they allow Senate passage by a simple majority of 51 votes, rather than the 60 needed to clear procedural hurdles.
The ruling means 16 lines will be stricken from the bill, Manley said, but any change required House action once again.
One of the changes was technical, and the other involved a provision to prevent reductions in the federal Pell Grant student aid program.
"We are confident the House will quickly pass the bill with these minor changes," said Kate Cyrul, a spokeswoman for Tom Harkin, Democratic chairman of the Senate Health Committee.
"These changes do not impact the reforms to the student loan programs and the important investments in education," she said.
The ruling came after Senate Democrats had killed 30 Republican amendments designed to derail the bill. The amendments were meant to force Democrats to cast difficult political votes before November's congressional elections.
Democrats methodically rejected them in an around-the-clock voting spree that started on Wednesday and stretched into the early hours of Thursday.
The Senate will resume debate later on Thursday and formally strike the provisions from the bill. It will conclude work on the amendments by mid-afternoon under an agreement between the Senate's majority Democrats and opposition Republicans.
The rejected Republican amendments included proposals to deny erectile dysfunction drugs to sex offenders, to ensure that insurance premiums do not increase under the law, and to prevent tax increases for families earning less than $250,000.
The Senate's approval of even one of the amendments also would have sent the entire package back to the House, and Democratic senators had vowed to prevent that.
"It's very clear there is no attempt to improve this bill.
There is an attempt to destroy this bill," Reid said as the non-stop voting entered its ninth hour. "Not a single one has been adopted. I don't know what they are trying to accomplish here."
The package of changes to the health care overhaul, approved in the House on Sunday, includes an expansion of subsidies to make insurance more affordable and more state aid for the Medicaid program for the poor.
It also would eliminate a controversial Senate deal exempting Nebraska from paying for Medicaid expansion costs, close a "doughnut hole" in prescription drug coverage and modify a January deal on a tax on high-cost insurance plans.
The final package would extend taxes for Medicare, the federal health insurance program for the elderly and disabled, to unearned income. It also includes reform of the student loan program.
The overhaul signed by Obama represents the biggest changes to the health system in four decades. It expands insurance coverage to 32 million Americans and imposes new regulations like barring insurance companies from refusing to cover patients with pre-existing medical conditions.
