The agency is attributing the loss of the correspondence to a computer crash.
Ms. Lerner ran a division of the IRS accused of unfairly scrutinizing conservative groups' applications for tax exempt status. She retired last year as a result of the scandal.
Rep. Dave Camp, chairman of the House Ways and Means Committee, said, "The fact that I am just learning about this, over a year into the investigation, is completely unacceptable and now calls into question the credibility of the IRS's response to congressional inquiries."
"There needs to be an immediate investigation and forensic audit by Department of Justice as well as the Inspector General," Camp added.
The House Ways and Means Committee had been heading up a Congressional Investigation of the IRS targeting scandal and recently voted to find Lerner in contempt for refusing to testify under oath.
For the IRS's part, the agency is claiming it's gone out of its way to retrieve the emails in question.
"The IRS has made unprecedented efforts in connection with this effort, producing more than 750,000 pages of documents to help complete the investigations. In total, the IRS's efforts to respond to Congress have involved more than 250 IRS employees working more than 120,000 hours at a direct cost of nearly $10 million," reads a statement released by the agency.
But despite the tens of thousands emails the IRS has been able to collect, mostly by scouring the computers of 83 other employees according to the agency, Camp's office insists that there are thousands of emails still missing, mostly between Lerner and outside agencies, "such as the White House, Treasury, Department of Justice, FEC, or Democrat offices."
According to the IRS, the computer crash in question occurred in 2011, prior to the the targeting scandal coming to light, and though Lerner attempted to have the hard drive in questions salvaged, IT staff were unable to recover the data because sectors of the drive had gone bad.
"Frankly, these are the critical years of the targeting of conservative groups that could explain who knew what when, and what, if any, coordination there was between agencies," Mr. Camp said. "Instead, because of this loss of documents, we are conveniently left to believe that Lois Lerner acted alone."