Reports of his resignation from the directorships came as the Justice Leveson Inquiry continued to hold public depositions about phone-hacking, which, deponents alleged, went beyond the now closed News of the World tabloid from the Murdoch stable.
According to recent filings at the Companies House, James Murdoch has steppe down from the boards of both News Group Newspapers Limited, publisher of The Sun; and Times Newspapers Limited, which operates The Times and Sunday Times.
NGN was the publisher of the News of the World, the Evening Standard reported.
Murdoch is likely to come in for criticism in the report of the culture, media and sport select committee of the House of Commons. The report is expected to be released in the near future, and any criticism may strengthen calls for Murdoch to resign from the company's shareholders.
"The departures come as James Murdoch also faces calls to quit as chairman of BSkyB at next week's annual general meeting. His decision means no member of the Murdoch family now sits on the boards of the flagship UK papers," the Evening Standard report said.
A News International spokesman said: "James Murdoch doesn't step back from NI. He remains chairman".
Murdoch continues as the executive chairman of News International, chairman of BSkyB, director of Times Editorial Board and deputy chief operating officer of News Corp.
Mark Lewis, lawyer representing the family of murdered teenager Milly Dowler, told the Levelson Inquiry on Wednesday that phone hacking was more widespread than just the News of the World.
"In a way, I feel sorry for the News of the World, or certainly the News of the World's readers," Lewis said. "Because it was a much more widespread practice than just one newspaper."