"It wasn't authorized by Congress," Trump said of the payments to the Journal. "I'm going to have to make a decision."
A White House spokesman said a final decision on the payments has not yet been made.
The federal government continues to make payments to insurers while the Republicans' lawsuit, filed against the Obama administration, is in limbo. A federal judge ruled in favor of Republicans, but the Obama administration quickly appealed the decision. Recently, Republicans asked for the case to be delayed, in light of GOP efforts to repeal and replace Obamacare.
According to the Kaiser Family Foundation, more than 6.4 million Americans were covered by reduced-cost insurance plans last year because of the federal CSRs.
If these payments stop, insurers in the individual market will be left without reimbursement for providing lower premiums and deductibles to low-income consumers.
Health care experts say the move would lead many insurers to flee the exchanges, which could end up collapsing. Insurers that stay would probably raise premiums, leaving consumers in the individual marketplace with bigger bills.
In a letter to Trump on Wednesday, America's Health Insurance Plans, a large insurance trade group, called on the White House to "remove uncertainty" about continuing the payments.
"This funding helps those who need it the most access quality care: low- and modest-income consumers earning less than 250 percent of the federal poverty level. If CSRs are not funded, Americans will be dramatically impacted," the letter read.
According to AHIP, cutting off the payments would cause many Americans to lose coverage, force insurers to raise costs and drive up premiums for all health insurance consumers.
ABC's Gillian Mohney contributed to this report.