The Medicaid program, which relies on both federal and commonwealth funds, could run out of the grant money as early as the end of 2016, three years earlier than anticipated, Mr. Rivera said. This could mean that 900,000 people will have to be dropped from the program.

Puerto Rico cannot use the federal health insurance exchange under the Affordable Care Act, and it chose not to create its own exchange because its citizens do not pay federal income taxes and thus are not eligible for the subsidies that make exchange plans more affordable.

A spokesman for the Centers for Medicare and Medicaid Services said the agency was aware of the growing concerns and was working weekly with a group of politicians, health care officials, advocates and insurance companies here to find solutions. So far, none have been offered.

The reduction in Medicare Advantage funding is meant to bring federal payments for that program more in line with traditional Medicare fee-for-service rates in Puerto Rico. Advantage plans on the mainland have received cuts in recent years for the same reason, although generally not as big.

But Puerto Rican officials and health care experts have long criticized the federal formula for calculating its fee-for-service rates as unfair, and point out that even the Virgin Islands, a much smaller commonwealth, gets considerably more money for Advantage.

Puerto Rican lawmakers and doctors warn that it will be more expensive for the United States to ignore the problem for one reason: Those who need medical care can quickly settle with relatives on the mainland, where it is pricier.

“My message to the federal government is simple: If you continue to treat Americans living in Puerto Rico poorly, they will exercise their rights and move to the U.S. mainland, where they will immediately be entitled to equal treatment,” said Pedro R. Pierluisi, Puerto Rico’s nonvoting delegate in the House of Representatives.