Read: EHR use more than doubles

The rule is also subject to a 90-day comment period, during which providers can voice concerns.

"Most importantly we are seeking additional public comments and plan for active engagement of stakeholders so we take time to get broad input on how to improve these programs over time," said Dr. Patrick Conway of the Centers for Medicare and Medicaid Services (CMS).

But Republicans on Capitol Hill are voicing opposition to the rules nonetheless, saying the government is imposing rules without understanding their effect on the health care system.

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“The administration has a tin ear,” Sen. Lamar Alexander, R-Tenn, the chairman of the Senate’s health committee, said in a statement Tuesday. “They’ve missed a golden opportunity to develop bipartisan support in Congress... Instead, they’ve rushed ahead with a rule against the advice of some of the nation’s leading medical institutions and physicians.”

But the Obama administration insists that it's time to finally make the adoption of EHRs universal.

The president has been pushing for wider use of EHRs since the first months of his presidency, when incentives for providers that adopted EHR were included in the HITECH Act of 2009, part of the stimulus package.

Medical advocacy groups and some members of Congress are saying that the problem is that many EHR systems simply don't work well, and that doctors often can't talk about it.

A bipartisan group in the Senate is working on a bill focused on "gag clauses" that vendors often demand of providers. Such contract stipulations prevent doctors from publicly discussing problems they've had with their EHR systems.

“If you have a product which just does not work, the pro­vider can’t tell any­body about that,” Sen. Bill Cas­sidy, R- Louis., told Na­tion­al Journ­al last week. “And so you have tax­pay­er-sub­sid­ized products ba­sic­ally—be­cause people are get­ting such heavy sub­sidies to pur­chase them—which don’t work, but no one can know it.”

Robert Wergin, president of the American Academy of Family Physicians, said the administration should demand more of vendors. “We believe this is the fault of the vendors and their lack of accountability while reaping huge profits from the HITECH act,” he said in a statement. “Vendors, not providers, must be held fiscally accountable for not yet achieving an appropriate level of interoperability.”