Werfel has spent plenty of time recently on Capitol Hill being questioned by lawmakers about why the agency targeted conservative groups that were seeking tax-exempt status for extra scrutiny.
The change is called for under the Vacancies Reform Act that requires that certain presidentially appointed, Senate-confirmed offices, including the commissioner of IRS, may be filled on a temporary basis.
When the president nominates a commissioner, Werfel's title will shift back to acting commissioner, Lew said.
"As you know, we have taken aggressive steps to address the issues that have arisen at the Internal Revenue Service," Lew says in the letter. "We are firmly committed to keeping Congress informed with respect to the actions we are taking.
Werfel recently took over for the former acting commissioner Steven Miller, who was asked by Obama to resign in light of the emerging problems at the agency.
“We have a great deal of work ahead of us to review and correct the serious problems that have occurred at the IRS and continue the important work of the agency on behalf of taxpayers,” Werfel said recently.
He is tackling a 30-day review of the agency at the request of Lew.