Republicans investigating the IRS targeting scandal said Wednesday that the agency continued to conduct secret surveillance on tea party groups even after approving them for tax-exempt status.

Acting Commissioner Danny Werfel said he shut down the monitoring program after he found out about it, and said he has halted all audits of tax-exempt organizations based on political activity as he tries to get a handle on the embattled agency.

Mr. Werfel, who was tapped four months ago to clean up the Internal Revenue Service after the targeting came to light, also told Congress he is troubled by emails sent by Lois G. Lerner, the woman at the center of the targeting scandal, that raise questions about her behavior. He said he has asked internal investigators to follow up on those emails.