WASHINGTON — Representative Darrell Issa of California, the Republican who is leading one of the investigations into the Internal Revenue Service’s scrutiny of Tea Party groups, accused the I.R.S. commissioner on Monday of lying, an allegation that only deepened the partisan mistrust about the motivations behind the numerous congressional inquiries into the matter.

The hearing on Monday night, before the House Oversight Committee, was the second time in four days in which the commissioner, John Koskinen, was called to Capitol Hill to explain what had happened with the emails. He testified on Friday before the Ways and Means Committee in an appearance that also turned confrontational.

Mr. Issa said Mr. Koskinen intentionally misled lawmakers when he testified in March that he would produce all the emails sent by Lois Lerner, the former agency official at the center of the controversy. Mr. Koskinen took over the I.R.S. after a previous commissioner was dismissed in the wake of the scandal over whether workers had unfairly singled out conservatives.

The I.R.S. acknowledged a week and a half ago that it had lost Ms. Lerner’s emails because of a large-scale computer failure, incensing congressional Republicans who were already deeply skeptical of the Obama administration’s insistence that there was no orchestrated effort by the I.R.S. to target political opponents.