Dick Fedorcio stood down a week after the Metropolitan Police said it would start proceedings against him for hiring Neil Wallis, a former deputy editor at the now-closed paper, as a media consultant.
It is the third major resignation from Scotland Yard, after the head of the force and another senior policeman stood down in July last year at the height of the scandal.
An initial 2006 police investigation into hacking led to the jailing of a News of the World journalist and a private detective, but the tabloid insisted it was a one-off.