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Governor Charlie Baker on Tuesday came out against a revised health care overhaul drafted by Washington, D.C., Republicans, warning that the legislation would result in “a massive loss of critical funds for the Commonwealth.”

Baker said in a statement he hopes Congress “reconsiders this amended legislation,” and his top spokesman underscored the administration opposes the bill that could come up for a vote in the US House of Representatives as soon as this week.

Baker also expressed thanks for the federal government’s willingness to grant the state flexibility in how it administers the Medicaid system, which pays for health care for the poor and disabled — with costs generally split between Massachusetts and the federal government.

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And, Baker said, his administration will continue to protect the state’s current health care system.

But his stance against the bill again puts the Republican chief executive at odds with his national party and President Trump, for whom Baker has said he did not vote.

In March, the governor had warned that an earlier attempt to repeal the Affordable Care Act — known more broadly as Obamacare — could put a half-million Massachusetts residents at risk of losing coverage, blow a $2 billion hole in the state budget, and threaten the state’s first-in-the-nation commitment to universal health care coverage.

The earlier version was pulled after it became clear it would not pass.

House Republicans have since changed the bill in order to draw more votes from hard-line conservatives, who helped scuttle the earlier effort. But the new legislation’s prospects remained unclear Tuesday. A running list of the stated positions of key representatives kept by HuffPost shows House Speaker Paul Ryan may not yet have locked up sufficient support among his GOP lawmakers. Several moderates, including Republican members of Congress from New York and California, remain undecided.

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No Democrats — including all nine Massachusetts representatives — are expected to vote for it.

And any bill that clears the House is likely to be radically altered in the US Senate, where Republicans hold a much slimmer edge.

Baker is in a unique position.

Massachusetts’s health care system is hugely reliant on federal aid and the flexibility the US Department of Health and Human Services has granted the state.

Trump oversees that department and has shown a predilection for being vindictive toward people who speak out against him, or who are seen as crossing him.

But the Baker administration’s analysis has found the GOP bill would have a negative impact on residents and on the state budget.

The governor is expected to run for reelection in 2018 and already has Democratic challengers.

Massachusetts has long been a leader in health care reform. Its sweeping 2006 law — signed by Mitt Romney, the state’s Republican governor at the time — created near-universal coverage for the state’s residents. Among its key components: a mandate that every resident get health insurance.

Major aspects of the federal health care law the GOP is working to repeal were based on the Romney-backed law.

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Here’s Baker’s full statement Tuesday:

“Our administration will continue to protect Massachusetts’ health care system, which leads the nation in health care coverage, and while the AHCA [American Health Care Act] bill has been amended, it would still result in a massive loss of critical funds for the Commonwealth. In the meantime, I am thankful for the federal government’s willingness to work with Massachusetts to deliver greater flexibility through the Medicaid system and I hope Congress reconsiders this amended legislation.”

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Joshua Miller can be reached at joshua.miller@globe.com. Follow him on Twitter @jm_bos and subscribe to his weekday e-mail update on politics at bostonglobe.com/politicalhappyhour.