Obama sought a significant budget increase for the IRS for next year, when the agency will start doling out subsidies to help people buy health insurance on state-based exchanges. Congressional Republicans, however, see management problems at the IRS as an opportunity to limit the agency's funding just as it is trying to put in place the massive new law.
Republicans have been fighting the health care law ever since Democrats enacted it in 2010 without a single GOP vote. Unable to repeal the law, some Republicans hope to starve it by refusing to fund its implementation.
The IRS scandals are giving them a timely excuse.
"I think it's safe to say they're not going to get the kind of increase they're asking for," said Rep. Ander Crenshaw, R-Fla., chairman of the House appropriations subcommittee that funds the IRS.
"The question is, based on their bad behavior, are they going to end up with less money?" Crenshaw said.
Last month, the IRS was rocked by revelations that agents had targeted tea party and other conservative groups for extra scrutiny when the groups applied for tax-exempt status during the 2010 and 2012 elections. A few weeks later, an inspector general's report said that the agency had spent lavishly on employee conferences during the same time period.
From 2010 through 2012, the IRS spent nearly $50 million on employee conferences. In 2010, the agency used money that had been budgeted to hire enforcement agents to instead help pay for one conference that cost $4.1 million, according to the watchdog's report.
Three congressional committees and the Justice Department are investigating the targeting of conservative groups, and much of the top leadership at the IRS has been replaced.
Obama appointed a new acting IRS commissioner, Danny Werfel, a former White House budget official. Werfel is conducting an internal review of the agency and is expected to issue recommendations for changes by the end of June.
All this is happening as the agency works to implement the health law that includes some of the most sweeping changes to the tax code in a generation.
"The IRS needs to repair the plane while it's in flight right now," said Paul Cherecwich, chairman of the IRS Oversight Board, an independent board within the agency. "Should the current budget environment continue, the IRS will have to continue to have to do more with less while rebuilding taxpayer trust. It has no choice, and it won't be easy."
Like many federal agencies, the IRS has seen its budget and workforce shrink since 2010, when the agency was allotted $12.1 billion. This year, the IRS is expected to spend $11.2 billion. Obama's proposed budget for next year is $12.9 billion - a 14 percent increase over current spending.
About $440 million would go toward implementing the health care law. That would include hiring nearly 2,000 employees, according to an analysis of the president's budget proposal by the Government Accountability Office.
"We are working to get to the bottom of what happened at the IRS, hold the responsible parties accountable, make sure it cannot happen again, and restore public trust and confidence in the IRS and its ability to administer the tax code fairly and efficiently," said White House spokeswoman Amy Brundage.
"For years Republicans in Congress have made repeated attempts to stop and slow down the Affordable Care Act. This is just the latest attempt to put up roadblocks to implementing the law," Brundage said. "The health law is the law of the land, and we are working to implement it well, so millions of Americans will have access to affordable and quality insurance."
Starting next year, the IRS will administer subsidies to help millions of individuals buy health insurance. The subsidies, technically tax credits because they are administered through the tax code, will help low- and middle-income families buy health insurance through the state-based exchanges.
Under the new law, nearly everyone in the U.S. will be required to have health insurance starting in 2014, or face penalties. The IRS will collect those penalties.
About 6 million people are expected to get the insurance subsidies next year, and that number will grow to 20 million by 2017, according to estimates by the nonpartisan Congressional Budget Office.
The enrollment season to buy health insurance through the exchanges starts Oct. 1.
"The bottom line here is that the IRS can barely manage what it already has to do, and that's a generous characterization given the targeting of conservative groups," said Sen. Orrin Hatch of Utah, the top Republican on the Senate Finance Committee, which oversees the IRS.
"Adding Obamacare under the IRS, that can only be described as a looming disaster," Hatch said. "And now the Democrats are saying we need to give the IRS more money. I'm not sure I'm willing to do that."
Democrats in Congress say they are growing tired of Republican attempts to repeal a law that has survived a review by the Supreme Court and whose main champion - Obama - won re-election last year.
"The American people will see over the next six months the lengths the Republicans will go to destroy the implementation of the Affordable Care Act," said Rep. Jim McDermott of Washington state, a senior Democrat on the House Ways and Means Committee. "I've expected it from the first day this (IRS) issue came up."
"I'm sad about it, it's awful," McDermott added. "But sometimes in a democracy people have to learn the hard way, and the American public is going to learn."