The Evening Standard reports that Companies House records show that Murdoch is no longer on the board of News Group Newspapers (NGN), which publishes The Sun, and Times Newspapers Limited (TNL), which publishes The Times and The Sunday Times.
The move means that no member of Rupert Murdoch's family now sits on the board of News International's major British newspapers, following stinging criticism in the phone hacking scandal.
News Group Newspapers also previously operated the News of the World, which was shut down in July after a string of allegations of hacking and criminality.
Tom Mockridge, the former chief of executive of Sky Italia who replaced Rebekah Brooks as boss of News International in July, has taken over from Murdoch at NGN and TNL.
Murdoch remains as executive chairman of News International, despite widespread criticism of his handling of the phone hacking scandal.
A News International spokesman said: "James Murdoch doesn't step back from NI. He remains chairman."
Murdoch also remains as director of holding company NI Group Limited and retains his seat on Times Newspapers Holdings, the independent editorial board set up in 1981 after his father Rupert bought The Times and The Sunday Times.
However, The Evening Standard claims that sources close to Murdoch have indicated that he now has a more hands-off role at both organisations.
Claire Enders, founder of media research service Enders Analysis, told the newspaper that James Murdoch is right to step back from these responsibilities, but the move won't stop questions over his leadership.
"Because it is inescapable that there will be some kind of censure from the [House of Commons] Culture, Media and Sport select committee, it is inevitable that people will say maybe you've got too much on your plate, it makes sense to step back from some of the roles," said Enders.
"He can step down from all these positions but he won't stop any of the other issues surrounding his stewardship."
Next week, Murdoch is expected to face a stern challenge to his future as chairman of Sky at the pay-TV giant's annual meeting, as shareholders prepare to show their disquiet at his connection to the hacking scandal.