Republicans on Wednesday released an email from the former IRS official's account from last year warning colleagues to be cautious in their messages because Congress could subpoena them.
In the email to a technology officer, Lerner also asked if instant message chats were searchable.
He added: "She didn't want an audit trail of what they were doing. And what they were doing is targeting conservatives for their views, no question at all."
Issa said the email brings into question whether Lerner purposely concealed documents from Congress.
"So at that point, was she also being cautious in what she considered making available vs. what went in the shredder?” he asked.
In the email, dated April 9, 2013, the IT official said chat messages are not necessarily searchable but can be saved as an email, in which case they would be subject to records requests. The IT officer advised that workers should assume the conversations would be saved.
Lerner replied, "Perfect."
"This is Lerner clearly cautioning and being delighted that instant chat wasn't tracking what they said," Issa said.
The latest email revelation was just one in a series of disclosures by Republicans in their more than year long investigation into the Internal Revenue Service's targeting of some conservative groups when applying for nonprofit status.
Earlier this year, it was revealed that Lerner's hard drive crashed in 2011. However, thousands of emails could still be retrieved.
"It is very clear [in] April 9, 2013, well into this investigation, she is still on the job and still covering her tracks or considering, if you will, whether they are covered,” he said.