This article is by Jeremy W. Peters, Michael Barbaro and Javier C. Hernandez.

Joel I. Klein, the former New York City schools chancellor, was in a tricky position. Three weeks ago, Rupert Murdoch asked Mr. Klein, now his trusted deputy, to oversee an investigation into the phone hacking scandal that has deeply wounded the News Corporation and its chairman, something Mr. Klein was eager to avoid.

“I am trying to get as far away from this as I can,” he lamented to a friend.

He has not succeeded. Mr. Klein, who joined the News Corporation as a senior vice president in January, is not only responsible for the investigation that could uncover what company managers knew about the hacking, but he also has become one of Mr. Murdoch’s closest and most visible advisers throughout the crisis.

His seemingly contradictory roles — de facto chief of internal affairs officer and ascendant executive with Mr. Murdoch’s ear — are raising questions about how robust and objective the internal inquiry can be. When Mr. Murdoch summoned a team of top deputies and outside consultants to London to help him manage the fallout from the hacking, Mr. Klein was one of the first to arrive, moving into a temporary office 20 feet from the chairman’s.

When Mr. Murdoch and his closest advisers debated whether to accept the resignation of Rebekah Brooks, a newspaper executive at the center of the controversy, Mr. Klein pushed for her exit. When Mr. Murdoch wrote a statement to deliver to Parliament last week, Mr. Klein weighed in on the drafts.