Ten current and former senior staff at the paper have been arrested since November in connection with alleged corrupt payments to public officials.
Sun journalists are angry at the way police were handed information by a News Corporation committee.
There have been questions raised about how this affects journalists' sources.
Last year News Corporation closed the News of the World over impropriety.
Revelations that staff employed by the newspaper hacked the phones of public figures prompted the closure of the 168-year-old paper.
Mr Murdoch, who is the chief executive of News Corporation, arrived on a private plane at Luton Airport from the US on Thursday evening.
He was taken to Wapping in a vehicle with blacked-out windows.
The BBC's Tim Reid, who was outside the company's headquarters in east London, said Mr Murdoch was expected to reassure staff about his commitment to the paper and its future but those inside were very much viewing the discussion as a "crisis meeting".
The meeting follows anger at the way in which the News Corporation's Management and Standards Committee set up to investigate allegations of wrongdoing at the Sun passed on information to the police.
The National Union of Journalists has said news organisations have a duty to protect their sources, and is considering a legal challenge to the company.
Media commentator Steve Hewlett told the BBC Mr Murdoch's relationship with the Sun was an emotional one, but that he was a businessman first.
He said the corporation had no option other than to be seen to "clean house", angering journalists by putting at risk traditional loyalties.
"They are creating wider concerns about handing information about journalists' contacts to police just because an internal committee thinks there may have been a payment that was illegitimate or unlawful to a public official."
He said the internal committee was not differentiating between suspect relationships and those in the public interest, such as "a £50 lunch that helped to discover troops in Afghanistan are woefully equipped".
The paper's former political editor Trevor Kavanagh used his Sun column to question the management's actions.
Writing in the Sun's sister paper, the Times, human rights lawyer Geoffrey Robertson said newspapers had a legal and moral duty to protect their sources.
Mr Murdoch has previously said he would not close the Sun.
Bob Satchwell, director of the Society of Editors, told the BBC that investigations in the name of public interest could suffer because of the concern about journalists' sources and what could happen to them.
He said: "Here, in an attempt to clear up past mistakes and to try and set records straight and to be open - you get into the stage where there is a chilling effect on journalism."
He said there had been a great deal of "conjecture" and allegations but "precious little solid evidence" and, until the latter was found, mistakes would be made along the way.