She did not disclose in that letter the IRS targeted conservative groups, even if for nonpolitical reasons.
Separately, a dozen U.S. senators led by Sen. Orrin Hatch, R-Utah, and Sen. Rob Portman, R-Ohio, sent Shulman a letter asking for more information about this situation.
Shulman's six-year term ended in November and the agency is currently led by interim commissioner Steven Miller.
IRS response sometimes took years
The leaders of several conservative groups told CNN on Friday about the IRS' questions.
Eric Wilson, executive director for the Kentucky 9/12 Project, said he was initially promised a response to his tax-exempt filing within 90 days, but instead received an 88-question inquiry asking for what he described as "far-reaching information."
They wanted membership lists and detailed information about directors of the group, such as their private activities outside the organization, he said. They also requested copies of pages on their website and social media accounts, such as Facebook and Twitter.
To comply with every request, Wilson said it would have required 5,000 printed pages. "They were trying to bury us in time and money," he said.
Wilson responded with a one-page letter, saying the questionnaire was beyond normal requests and they would not comply. He started noticing posts online and heard from like-minded conservative groups that they were receiving similar questions from the IRS.
His December 2010 filing was met with a final response just a month ago, on April 1, when the IRS sent him a 200-word letter stating his group had been designated a 501(c)(4) organization with no explanation for the delay.
In Ohio, the Portage County TEA Party was experiencing similar issues. Executive Director Tom Zawistowski said it took his group nearly three years - June 2009 to December 22, 2012 - to receive approval from the IRS.
He filled a four-inch thick binder with materials requested by the IRS, including speakers lists and printouts of every page from its website and Facebook page, every tweet.
His group and 26 others worked with the Washington-based American Center for Law and Justice, which lobbied for action to be taken on the matter.
While conservative groups were the targets, the IRS' Friday admission drew reaction from both sides of the aisle.
House Majority Leader Eric Cantor announced Friday the House would investigate the matter, saying in a statement "the IRS cannot target or intimidate any individual or organization based on their political beliefs."
Senate Republican Leader Mitch McConnell called on the White House to conduct "a transparent, government-wide review" to ensure similar practices weren't being carried out at other agencies.
McConnell, who called an apology from the IRS insufficient, deemed the IRS tactics "political thuggery" with no place in American politics.
The left-leaning American Civil Liberties Union also called out the IRS, saying in a statement, "Even the appearance of playing partisan politics with the tax code is about as constitutionally troubling as it gets."
Tea Party groups were similarly incensed. The Tea Party Patriots, one of the nation's largest, rejected an IRS apology and insisted on resignation from the officials involved in the targeting.
Carney told reporters on Friday that the additional scrutiny was "inappropriate."
"We would fully expect the investigation to be thorough and for corrections to be made in a case like this," Carney said. "I believe the IRS has addressed that and has taken some action, and there's an investigation ongoing."
Issa, the congressman whose committee requested the audit, said in a joint statement with another committee member that they "will aggressively follow up on the IG report and hold responsible officials accountable for this political retaliation."
The Democratic chairman of the Senate Permanent Subcommittee on Investigations, Sen. Carl Levin, also said an investigation into the matter was required.