A bipartisan deal to fund Obamacare payments stalled in the Senate Wednesday after President Trump derided the payments as "bailouts," but Republicans behind the package are trying to keep the deal alive.

In addition to Trump, who tweeted that he opposes the agreement Wednesday morning, members of Senate leadership on Wednesday cast skepticism about the deal brokered by Sens. Lamar Alexander, R-Tenn., and Patty Murray, D-Wash., to fund the insurer payments for two years in exchange for changes to the law.

"We are kind of in a holding pattern right now until there is some kind of a breakthrough between the president and Sen. Alexander," said Sen. John Thune, R-S.D., the third-ranking Republican senator. "That could happen sooner, but it also could be a December issue."

He said the deal could be included in an omnibus spending deal that must be passed to prevent a government shutdown in December, or it could be included in another must-pass vehicle sooner if President Trump jumps on board.

Related: Key questions about the Senate's Obamacare subsidy deal

Sen. John Cornyn, R-Texas, the number two ranking senator, applauded the effort of Alexander and Murray but said, "I think this is the beginning of a longer conversation. Until the president is on board, yes, probably some changes need to be made to satisfy the president."

But it is not clear what those changes will be or when they can be made.

Alexander and Murray announced the agreement on Tuesday after Trump encouraged Alexander to resume talks on a short-term deal to stabilize Obamacare's exchanges. Alexander said Wednesday he hopes to get the bill on the Senate floor by Thursday.

But on Wednesday morning, Trump tweeted that he couldn't support any bill that would bail out insurance companies. That has been a common criticism from Republicans on the cost-sharing reduction payments, which pay insurers for reducing the cost of co-pays and deductibles for low-income Obamacare customers. Trump said last week he would cut off the payments Oct. 18.

Less than two hours after the tweet, a spokesman for House Speaker Paul Ryan said that he couldn't support the deal either and that the Senate should continue to work on repealing and replacing Obamacare.

The tweet and Ryan's opposition did not deter Alexander.

He told reporters that the bill contains some stiff provisions to ensure cost-sharing reduction payments benefit consumers more than insurers.

Insurers are required to lower the out-of-pocket costs for those customers. Without the payments, they have said they will raise premiums for everyone on the law's exchanges.

The bill states that for a cost-sharing reduction payment to go to an insurer, a state has to submit a plan showing how those payments would benefit consumers and the federal government, according to a Senate aide. Some ways to do that include monthly rebates or other means of providing direct relief to customers.

Alexander said that neither he nor Murray are interested in bailing out insurance companies.

"We have strong language in the Alexander-Murray agreement that consumers get the money, not the insurance companies, and if the administration has stronger language we will put it in," he said.

Murray gave a more measured response when asked by reporters if she was open to further changes.

"We put together principles that we absolutely agree on," she said. "If there are provisions that strengthen anything for consumers, of course, but at this point we stand with our principles."

Senate Minority Leader Chuck Schumer told reporters that they shouldn't reopen talks since the package that was produced was good.

Whether the bill will reach the Senate floor is not known. Schumer hinted that the deal could be part of another must-pass vehicle, such as a spending bill, but he would like to see it done sooner rather than later.

Without the legislation, insurers likely will charge higher rates for 2018. An estimate from the nonpartisan Kaiser Family Foundation pegged an average rate hike of 20 percent on the most common Obamacare plan.

Sen. Mike Rounds, R-S.D., a co-sponsor of the bill, said many Republicans agree with the president and want to ensure the bill does not provide federal money to bail out the insurance companies.

"What the president is expressing is what a lot of us have expressed," Rounds told reporters Wednesday. "We want it to be clearly defined within law, that the money has to be expended to take care of those people that it is intended for. We think the president brings up a good point and we think the legislation will specifically address the concerns that he has because it is the same concern that we have as well."

Some senators are still open to the deal, including Sen. Tim Scott, R-S.C., who wants to bolster flexibility options for states.

"This is a strong step in the right direction," he said. "My support of it is not quite there yet."

But several senators are outright opposed to the legislation and don't appear that they can be convinced.

"It would last two years, spend a whopping amount of money and not solve the problem and lead us down a path of never getting the problem done," said Sen. Orrin Hatch, R-Utah, chairman of the Senate Finance Committee. "I have trouble with it."

Sen. Ted Cruz, R-Texas, suggested he also opposes the legislation.

"I don't think we should be bailing out giant insurance companies," Cruz said. "That would be a mistake."

Others were concerned they were propping up a collapsing law.

"I don't want to vote to just put paint on rotten wood," said Sen. John Kennedy, R-La.