Archbishop John Nienstedt denies the allegations, but is removing himself from ministry pending an investigation.
The archdiocese says the incident allegedly occurred in 2009 after a confirmation ceremony. Nienstedt is accused of inappropriately touching an underage male on the buttocks during a group photography session.
The archdiocese learned of the allegation last week and instructed the person who brought it forward to go to police.
In a letter posted Tuesday on the archdiocese website, Nienstedt says the allegation is “absolutely and entirely false.” He says he hopes the investigation will be thorough and quick so he can return to work.