ST. PAUL — House Republicans put a health care program for tens of thousands of low-income Minnesotans on the chopping block as the centerpiece of a budget bill that aims to put up half of the $2 billion in tax relief GOP lawmakers hope to offer.

After a debate that stretched from Tuesday afternoon into Wednesday morning, the GOP-controlled House passed a bill that funds Minnesota’s health and human services department, the largest slice of the state’s $40 billion budget, but eliminates the MinnesotaCare program. The measure passed 72-60, with all Democrats voting against it.

The bill’s passage sets up a wide gulf with the Democrat-controlled Senate, where top lawmakers say going after MinnesotaCare, a program created in 1992 for residents who make too much money to qualify for Medical Assistance, when the state has a hefty budget surplus is unthinkable. It has sparked memories of 2005, when a GOP-led effort to tighten MinnesotaCare enrollment was a large factor in a government shutdown.

With changes that weed out ineligible enrollees from the state’s public programs and cutting administrative expenses at the Department of Human Services, the Republicans who control the House aim to make more than $1 billion in cuts to a sector of state government they say is spending too much money, too fast.

“The ship we’re on is heading for a waterfall,” said Rep. Matt Dean, chairman of the House committee that handles health care spending. “I think you know it, we know it, Gov. Dayton knows it.”

But the biggest savings, more than $500 million, come from axing MinnesotaCare. In its place, the GOP budget would offer a state-based tax credit to buy down private coverage as roughly 90,000 enrollees move to the health insurance marketplace starting next year.