The surprise move has fuelled expectations that he is preparing to sell the newspaper group.
Companies House filings show that Murdoch stepped down from the boards of the NI Group, Times Newspaper Holdings and News Corp Investments in the UK last week. He also quit a number of News Corp's US boards, the details of which have yet to be disclosed by the US Securities and Exchange Commission.
News Corporation played down the significance of the resignations as "nothing more than a corporate house cleaning exercise prior to the company split".
The media giant took a similar line when James Murdoch resigned a string of directorships at News International last November. He quit as chairman three months later.
News Corporation has already said it will split into two separately listed companies, distancing its embattled newspaper and book publishing interests from its rapidly growing film and television operations.