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The man who took on the IRS before the tea party grumbled

"I don't give a s--- about the tea party thing," Carl Malamud was saying the other day. "And I don't personally believe it."

Malamud, a public domain advocate who once advised President Barack Obama's transition team, was referring to the ongoing controversy over whether the Internal Revenue Service unfairly targeted conservative organizations that had applied for tax-exempt status.

Many Republicans, including GOP leaders in Congress, have claimed a major scandal s brewing. Malamud doesn't think so, but he does find common cause with his right-leaning brethren over a larger point: The IRS has a big problem keeping track of things.

In fact, even before conservatives took the IRS to court, trying to get former official Lois Lerner's missing emails, Malamud was waging his own legal battle against the agency. Although the suits are dissimilar in content, they have become intertwinedas things tend to be.

Alas, there are Republicans and Democrats, red states and blue states: But anger with the IRS seems to unite all.

"The way they use computers is very bad," Malamud told CNBC.com.

At issue for him are two general principles: what the IRS has failed to make public and how the IRS has failed to protect the public.

Malamud runs an open-government nonprofit, Public.Resource.Org, which puts online a trove of government documents, including court records, safety standards and the tax filings of nonprofit organizations. While the public is legally entitled to these records, they often prove tricky or cumbersome to obtain.

In an effort to make things more user-friendly, Public.Resource.Org has built huge archives, including the most comprehensive online archive of the 990 forms that tax-exempt organizations must submit to the IRS annually. These forms include information about an organization's balance sheet, revenue and expenses, as well as a listing of key officers, board members and their compensations.

Since 2007, Malamud's Web-based organization has become an essential tool for government and consumer watchdogs and journalistsand receives about 2 million downloads a month, according to its own figures. And according to Malamud, it has given him a particularly intimate familiarity with the bureaucratic incoherence and intransigence of the federal government.

Although he has run up against this beforein the 1990s, Malamud made his name when he cajoled the Securities and Exchange Commission to publish corporations' financial disclosure forms onlinehe has found the IRS to be "particularly uncommunicative."

Andrew Harrer | Bloomberg | Getty Images

Malamud began acquiring nonprofit tax forms from the IRS in 2008, eventually converting 98 pounds' worth of DVDs into digital files for the Web. In the course of this project, Malamud says he discovered countless examples of individuals' Social Security numbers being inadvertently released to the public because they weren't redacted from the forms. Several years ago, after hearing complaints from visitors to his website, Malamud began making the redactions himself and asked the IRS to do the same. (It is the nonprofit's legal responsibility to prevent individuals' tax identification information from being publicly disclosed, and Malamud has sent strongly worded letters to some of the worst offenders on this front.)

Read More IRS head and lawmakers clash over missing email

But he said these suggestions have gone largely unheeded. So recently, having grown fed up with the lack of a response, Malamud decided to start a not-so-subtle awareness campaign, sending White House officials and key congressional members, including Republican Rep. Darrell Issa, one of the IRS's biggest detractors over the Lerner case, thumbnail drives with tax forms showing how the privacy of average Americans is routinely being compromised. Last month, Issa, who chairs of the House Oversight and Government Reform Committee, marshaled Malamud's findings to further his case that the IRS under Lerner, was out of control.

Malamud also decided this month to take down temporarily his website's database of 990 forms, hoping this action would prick the consciousness of journalists and activists who use them.

"I am hoping a lot of them start picking up the phone and complaining to the IRS," Malamud told CNBC.com. "I want the IRS to deal with this situation. The easier thing for the government is if I have my data online and keep it up and running. That takes all the pressure off them. I hate hurting my friends, and I hate taking data offline, because that is not what I do."

The forms have become an increasingly important oversight tool since the Supreme Court ruling in Citizens United paved the way for an explosion of nonprofit political organizations. And it's in part why Malamud is pushing the IRS for more information than the organization appears willing to provide. Last year, Malamud filed a lawsuit in federal court asking that the IRS make public the same "machine-readable" versions of 990 forms that it receives from nonprofits. The IRS had previously denied his requests on the grounds that its internal rules don't require it to release forms in this way. It might seem like an esoteric dispute, but Malamud argues that this information—released in this format—is critical to allowing the American public to understand how its nonprofit sector works. And now, coupled with the Lerner dispute, it is reinforcing the notion that the agency has, as Malamud puts it, "an IT problem."

Read More IRS gave bonuses to employees who didn't pay their taxes

Last month, the IRS attempted to dismiss the case, but a federal judge in California allowed it to continue. The IRS did not respond to a request for comment for this story.

Malamud, who previously served as John Podesta's top technologist, when the current White House counselor was running the Center for American Progress, seems conflicted that his transparency activism has now cross-pollinated with conservative animus over the Obama administration.

"I know they would rather I drop this for a couple of years," said Malamud. "But I have been doing this before the tea party thing got started, and I think you have a moral obligation [to continue]."

"I have tried to paint this as an opportunity [for the IRS]: 'You are playing defense. Why don't you do something positive like release the e-file data?' And then people won't be looking so much at the IRS and might start looking at CEO compensation in nonprofits."

CORRECTION: This story was updated to reflect that John Podesta is a current White House counselor.

—By Daniel Libit, special to CNBC.com.

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