"CHIP should be part of a long-term solution, not a 30 Day, or short term, extension," Trump tweeted
That is the opposite to what his administration said on Wednesday.
"The Administration supports the bill's multiyear funding extension of the Children's Health Insurance Program (CHIP)," the Office of Management and Budget said in a statement. "If H.J. Res. 125 were presented to the President in its current form, his advisors would recommend that he sign the bill into law."
Trump's tweet -- which confounded even Trump's aides inside the West Wing -- threw negotiations over how to fund the government into chaos as a Friday deadline looms. Republicans, including those inside the Trump administration, had planned to use funding for children's health care program to woo Democratic votes for the short-term spending bill.
Hours after Trump's tweets a White House official issued a statement to reiterate that Trump supports the short-term spending deal being pushed by Republicans.
"The President supports the continuing resolution introduced in the House," said White House principal deputy press secretary Raj Shah. "Congress needs to do its job and provide full funding of our troops and military with a two-year budget caps deal. However, as the deal is negotiated, the President wants to ensure our military and national security are funded. He will not let it be held hostage by Democrats."
The statement, notably, doesn't mention the health care program.
A proposal to fund the government until mid-February unveiled by House GOP leaders earlier this week included a six-year reauthorization of the children's health insurance program, aimed at winning over key Democratic votes in the Senate.
The inclusion of the funding, aides said, was strategic and backed by the White House. Republican aides hope including the popular children's health care program would make it difficult for Democrats, particularly in the Senate, to oppose on both policy and political grounds. And for those that did, that vote would become a potent political issue for Republicans to attack on in the weeks and months ahead.
"I feel that it makes no sense for Democrats to try and bring us to a shutdown, to try and cut off CHIP funding for states that are running out of money like Minnesota, and Washington, and Kentucky, and other states," House Speaker Paul Ryan said Wednesday.
Senate GOP leaders will need roughly 10 Democrats to sign on to the measure to fund the government based on Senate rules requiring 60 votes to break a filibuster and advance.
Thursday is not the first time the President seemed to tweet a position contradicting a top administration official or previously announced White House policy.
Trump publicly suggested last fall that Secretary of State Rex Tillerson was "wasting his time" trying to negotiate with North Korea, and last week complicated a closely coordinated effort between his administration and congressional Republican leadership on a six-year extension of a section of the Foreign Intelligence Surveillance Act.
CHIP was first authored by late Democratic Sen. Ted Kennedy of Massachusetts and Republican Sen. Orrin Hatch of Utah. But it garnered significant support from then-first lady Hillary Clinton, who has recently slammed
Republicans who failing to reauthorize the program.
Despite the delay, though, both Republicans and Democrats have said they support funding the program.
"I think everybody across party lines wants to see our military funded. They want to see the CHIP program funded," Republican National Committee chairwoman Ronna Romney McDaniel said on CNN a few minutes before Trump's tweet.