The Trump administration announced two weeks ago that it would halt the subsidies, which reimburse insurers for reducing deductibles, co-payments and other out-of-pocket costs for low-income people.
The bill would provide money to continue the subsidies, known as cost-sharing reduction payments, through 2019.
The budget office said that part of the bill would not change its estimate of federal spending because it had already assumed that the government would pay the subsidies: $9 billion a year in 2018 and 2019, and a total of $99 billion from 2018 to 2027.
Under another part of the bill, most insurers would have to issue rebates to consumers and the federal government in return for receiving the cost-sharing reduction payments next year. The budget office estimated that the government would receive rebates from insurers totaling $3.1 billion as a result.
Payment of the cost-sharing subsidies would not affect premiums for 2018, which have already been set, but premiums in 2019 would be lower than if the subsidies were cut off, the budget office said.
The Alexander-Murray bill would make it easier for states to obtain waivers from requirements of the Affordable Care Act governing insurance markets. The budget office predicted that more waivers would be approved, but it said that it did not expect them to cause any significant change in federal spending.
Ms. Murray said the bill would prevent premium increases and “serious sabotage” of health insurance markets that would otherwise occur as a result of actions by Mr. Trump. The Trump administration says it has no legal authority to continue the payments on its own because Congress never explicitly provided money for them.