WASHINGTON — President Obama appointed Daniel I. Werfel, the controller of the Office of Management and Budget, to be the acting commissioner of the Internal Revenue Service, the White House announced Thursday.

Mr. Werfel, who manages much of the day-to-day operations at the budget office, will replace Steven Miller, who was fired this week as the agency’s interim director in the scandal over its targeting of conservative groups.

The White House said in a statement that Mr. Werfel would begin his new job on Wednesday.

“Danny has proven an effective leader who serves with professionalism, integrity and skill,” Mr. Obama said in the statement. “The American people deserve to have the utmost confidence and trust in their government, and as we work to get to the bottom of what happened and restore confidence in the I.R.S., Danny has the experience and management ability necessary to lead the agency at this important time.”

Another top official at the I.R.S. also announced his departure Thursday. Joseph H. Grant, the acting commissioner of the tax exempt and government entities division, said he would retire on June 3.