In a Wall Street Journal interview this week, Trump raised the possibility of shutting off the money if Democrats won't bargain on health care.
"Despite the pleas of consumers and the advice of experts, the Trump Administration is going full-steam ahead with its latest effort to try and sabotage the Affordable Care Act and is making health care less affordable, less accessible and less meaningful for America's families", he said in a statement.
Trump's new rules do not address so-called cost-sharing subsidies, which differ from the better-known tax subsidies for insurance premiums.
"I don't want people to get hurt", Mr. Trump said.
"I don't think Democrats will let this happen, but I frankly don't think the Republicans want it to happen either", said Timothy Jost, a health-law professor at Washington and Lee University.
So far, Democrats are taking the opposite approach - lashing out at Trump and instead demanding that the payments be included in an upcoming spending bill.
House Democratic leader Nancy Pelosi of California called that an "appalling threat". President Donald Trump could drop the Obama administration's appeal of the ruling and halt the payments.
The Trump administration has indicated that the payments will continue as long as the case is being litigated, but insurers want more of an assurance that these subsidies will be available next year.
A much tighter sign-up deadline and coverage delays will be waiting for some health insurance customers now that President Donald Trump's administration has finished a plan created to stabilize shaky insurance markets.
Numerous changes announced Thursday follow recommendations from insurers, who wanted the government to address shortcomings with HealthCare.gov markets, including complaints that some people are gaming the system by signing up only when they get sick, and then dropping out after being treated. While opening day would remain the same - November 1 - the final rule closes the marketplace on December 15 instead of at the end of January. Under the Affordable Care Act, there are a number of reasons someone might be eligible to sign up for coverage outside the normal enrollment period, such as moving, losing a job, getting married or having a kid.
If these payments stop, insurers in the individual market will be left without reimbursement for providing lower premiums and deductibles to low-income consumers.
"The rule should help improve the functioning of the individual market, and our members are thankful to see improvements on special enrollment periods and greater flexibility in product design", said Dominick Pallone, executive director of the Michigan Association of Health Plans. "They will help protect Americans enrolled in the individual and small group health insurance markets while future reforms are being debated".
The payments subsidize insurers for keeping out-of-pocket costs down for low income consumers, as mandated by the Affordable Care Act. "Under the new rule, patients trying to enroll in insurance plans outside of the annual enrollment period will face strict documentation requirements", ACS CAN president Chris Hansen said in a statement.
Obamacare includes a host of mechanisms to make buying insurance easier and more affordable for people who don't receive coverage through their employer and have to buy it on the individual market.
A federal district judge in a lawsuit brought by House Republicans found the federal payments for the cost-sharing reductions unconstitutional. Most urgently, health plans and the consumers they serve need to know that funding for cost-sharing reduction subsidies will continue uninterrupted. Far from forcing Democrats to the table to help him pass the Obamacare repeal-and-replace legislation he can not get with Republican votes alone, he has emboldened them to fight back. And Democrats are themselves keenly aware of the shifting dynamics, seizing every opportunity they can to insist Republicans now own the health-care law.