WASHINGTON — President Obama said on Thursday that he would nominate John A. Koskinen, a widely respected manager who took charge of a bankrupt Freddie Mac, to head another troubled institution, the Internal Revenue Service.

Should Mr. Koskinen win Senate confirmation — he is well regarded among lawmakers of both parties — he would become commissioner at a periodic low point for the tax-collection agency, after accusations from Republicans that it unfairly targeted conservative groups in screening their tax-exempt status.

Mr. Koskinen would fill the opening created when the Obama administration dismissed the acting I.R.S. commissioner, Steven T. Miller, in May after the controversy first surfaced. Mr. Obama’s treasury secretary, Jacob J. Lew, had installed Daniel I. Werfel as acting commissioner until a new tax chief could be nominated and confirmed.

“John is an expert at turning around institutions in need of reform,” Mr. Obama said in a statement. “With decades of experience, in both the private and public sectors, John knows how to lead in difficult times, whether that means ensuring new management or implementing new checks and balances.”