"Any agency is required to notify us when they realize they have a problem," Ferriero said.
Lerner is at the center of the controversy and has refused to answer questions from Congress, citing her Fifth Amendment right not to incriminate herself. In May, the House voted to hold Lerner in contempt of Congress. She retired from the IRS last fall after having been placed on paid leave.
In an effort to determine whether the Obama administration had any knowledge or involvement in the activities of the IRS division that reviews applications for tax-exempt status, lawmakers have sought and received thousands of IRS records — none of which has implicated the White House in the controversy. But when it was revealed that some of the emails sought were unrecoverable, Republicans questioned the timing of the hard drive crash, suggesting key records related to the investigation have conveniently gone missing.
IRS Commissioner John Koskinen has said that he has seen no evidence anyone committed a crime when the agency lost emails.
Pressed by a congressman Tuesday, Ferriero would not state that the IRS broke the law. He would only say that the agency didn't "follow" the law, referring to the Federal Records Act.
In a rare evening hearing before the same committee on Monday, Koskinen said there was no evidence that Lerner intentionally destroyed the missing emails. To the contrary, he said, the IRS went to great lengths trying to retrieve lost documents on Lerner's computer, even sending it to the agency's forensic lab.
Republicans have said the Obama administration has not been cooperative with Congress' investigation.
"They've not only not fully cooperated, they haven't done a damn thing to help us get to the truth of what really happened," said House Speaker John Boehner, R-Ohio. "Lois Lerner refuses to tell us the truth, and then all of sudden, 'Oh my goodness, we lose two years' worth emails.' Listen, I grew up in a bar. This doesn't pass the straight-face test."
Monday night, House Oversight Committee Chairman Darrell Issa, R-Calif., subpoenaed White House counsel Jennifer O'Connor to testify about her time at the IRS from May to November 2013. While at the IRS, O'Connor helped the agency gather documents related to the congressional investigation.
On Tuesday, when he questioned O'Connor, Issa called her a "hostile witness."
O'Connor disagreed. "I'm definitely not hostile," she said.
Later in the hearing, Issa said he consulted with another member who is a former prosecutor and the proper term to describe O'Connor was a "non-cooperative witness."
White House spokesman Josh Earnest said the White House has been cooperating throughout the investigation.
"Our commitment to cooperating with legitimate congressional oversight and in some cases illegitimate congressional oversight is pretty well documented," Earnest said. Asked if the House Oversight and Government Reform committee's investigation was "illegitimate," Earnest said, "I'm saying that there are legitimate questions that can be raised about the partisan motivation of some of those who are conducting oversight in this circumstance."
The IRS was able to generate 24,000 Lerner emails from the 2009 to 2011 period because she had copied in other IRS employees. Overall, the IRS said it is producing a total of 67,000 emails to and from Lerner, covering the period from 2009 to 2013.