Les Hinton has resigned as chief executive of News Corp's Dow Jones unit, hours after Rebekah Brooks resigned from her role as News International's chief executive.
Mr Hinton was the chairman of News International when News of the World journalists are alleged to have hacked peoples' phones.
More recently he headed the Dow Jones company, which publishes the Wall Street Journal.
In a statement Mr Hinton denied any knowledge of phone hacking but said as he was News International's head at the time of the alleged incidents he felt it proper he resign despite this.
Mr Hinton had worked for News Corp for 52 years and Mr Murdoch said his decision to resign was 'a matter of much sadness to me.'
Earlier Rebekah Brooks resigned as chief executive of News International, the British subsidiary of News Corp, following intense pressure for her to stand down over the phone hacking controversy.
Ms Brooks was Rupert Murdoch's most senior newspaper executive in Britain.
News Corp moved quickly to replace Ms Brooks by appointing Sky Italia's Tom Mockridge as the new chief executive of News International.
In an internal message to staff, Ms Brooks said she felt a 'deep sense of responsibility' for the crisis that erupted last week and resulted in the closure of News International's News of the World tabloid.
'I have given Rupert and James Murdoch my resignation. While it has been a subject of discussion, this time my resignation has been accepted,' wrote Ms Brooks, herself a former editor of the paper.
'As Chief Executive of the company, I feel a deep sense of responsibility for the people we have hurt and I want to reiterate how sorry I am for what we now know to have taken place,' she wrote.
'I have believed that the right and responsible action has been to lead us through the heat of the crisis. However my desire to remain on the bridge has made me a focal point of the debate.
'This is now detracting attention from all our honest endeavours to fix the problems of the past.'
FBI investigating 9/11 hacking claims
Meanwhile, the FBI is examining allegations that Rupert Murdoch's News Corporation may have tried to hack into the phone records of victims of the 11 September in the US in 2001.
US Attorney-General Eric Holder said the investigation followed requests from members of the US Congress on the issue.
One of the senior politicians to make representations was senior Republican Party Congressman Peter King.
Mr King, who represents an area in New York where many victims lived, said the allegations deserved to be fully looked at.
‘We are aware of the allegations and we are looking into it,’ a spokeswoman told AFP from the FBI's offices in New York, where specialised cybercrime and white collar crime units were expected to make the inquiries.
'For allegations into the 9/11 victims, this would be done out of New York,' a legal source told AFP, speaking on condition of anonymity because he was not authorised to speak about the case.
A US Justice Department spokeswoman said only: 'The department does not comment specifically on investigations, though any time we see evidence of wrongdoing, we take appropriate action.'
In the US, Murdoch's Fox News Channel is seen by many Democrats as a tool of their Republican rivals, while the network denies any bias.
So far, though, his more significant holdings in the United States have been unaffected by the scandal.
The phone hacking row had rumbled on for months but exploded last week after it emerged that the paper had targeted the messages of Milly Dowler, a murdered 13-year-old girl, and of the families of the veterans of the wars in Afghanistan and Iraq.
Mr Murdoch shut the 168-year-old tabloid on Sunday, and on Wednesday pulled out of the biggest media takeover bid in British history, for pay-TV giant BSkyB, before accepting to be grilled by lawmakers to try to limit the damage.
News Corp's shares have plummeted in the past week, and the Murdoch-owned Wall Street Journal reported that the media tycoon was considering selling off his remaining British newspapers, The Times, The Sunday Times and The Sun.
Murdoch to apologise in adverts
Rupert Murdoch will use adverts in UK newspapers tomorrow to apologise for the News of the World's 'serious wrongdoing'.
The media tycoon will personally say he is 'deeply sorry' for the hurt suffered by the people affected as he seeks to atone for the phone hacking scandal.
The advert will run in tomorrow's Daily Mail, Daily Telegraph, Financial Times, Guardian, Independent, Sun and Times, News International said.
A second advert will appear in newspapers on Sunday and Monday, outlining the steps that News International and parent company News Corporation have taken to investigate and address previous wrongdoing and prevent it from happening again.
Mr Murdoch gave a 'full and sincere apology' to the family of Milly Dowler today after meeting them over the News of the World's hacking of her mobile phone, the family's lawyer, Mark Lewis, said.
Meanwhile, former News of the World editor Andy Coulson stayed as a guest of British Prime Minister David Cameron at his country house in March.
Mr Coulson, who resigned as Downing Street director of communications in January, had dinner and stayed overnight at Chequers.
A No 10 source said: 'The Prime Minister invited him to thank him for his work.'
Mr Coulson was arrested last week over alleged corruption and phone hacking at the Sunday tabloid while he was editor. He was bailed the same day.
