In court papers, the IRS said the hard drive was destroyed after two sets of trained technicians tried to retrieve the data. The tax agency said it was standard procedure to destroy old data storage equipment that may have contained confidential taxpayer information.
The IRS says Lerner's computer crashed in 2011, destroying an untold number of emails. At the time, Lerner headed the division that handles applications for tax-exempt status.
Lerner is a central figure in congressional investigations into the handling of applications by tea party and other conservative groups.
IRS Commissioner John Koskinen had told Congress that Lerner's hard drive was recycled and presumably destroyed. Friday's court filings confirmed it.
As part of a lawsuit, U.S. District Judge Reggie B. Walton ordered the IRS last week to explain what happened to the hard drive.
Walton also wanted information about an inspector general's investigation into the lost emails. Walton wanted to know the qualifications of computer experts conducting the investigation, and he wanted a projection on when the investigation will be complete.
Timothy Camus, a deputy inspector general for investigations, said in court papers that 11 special agents are on the case. However, he added, "It is not possible to give an estimated date of completion."
A Justice Department lawyer told Walton last week that there was no evidence Lerner intentionally destroyed her hard drive.
On Thursday, Deputy Attorney General James Cole told Congress that the Justice Department is investigating the lost emails as part of a larger probe into the way agents handled applications for tax-exempt status.
Walton's order came in a lawsuit filed by a group called True the Vote, which says it advocates for the integrity of elections. The group sued the IRS over delays in its application for tax-exempt status.
Follow Stephen Ohlemacher on Twitter: http://twitter.com/stephenatap
Copyright 2014 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.