Less than a year into his tenure at the Justice Department, Attorney General Eric Holder Jr. is tasked with reshaping his command staff in the wake of the resignation of his second-in-command, David Ogden, who is stepping down amid what friends and department lawyers describe as a management clash.

Ogden, a ­former Wilmer Cutler Pick­ering Hale and Dorr partner who held senior positions in the Clinton administration Justice Department, announced Dec. 3 he is leaving his post as deputy attorney general in February. He plans to return to Wilmer’s government and regulatory litigation practice, which he co-chaired before taking a leave last year to run the Justice Department transition team under Barack Obama.