James Murdoch has appeared before the Leveson Inquiry, answering questions about his role at News International.
In an early exchange, the 39-year-old admitted that company's corporate systems failed to pick up on legal risks posed by its papers' methods of finding stories.
The media boss also told the inquiry into press standards that the News of the World should not have run its story falsely alleging that former Formula 1 boss Max Mosley had a "sick Nazi orgy".
Murdoch became executive chairman of News International when he took over his father's media empire in Europe and Asia in December 2007.
He was questioned about changes to the management culture he sought to introduce at the publisher.
Robert Jay QC, counsel to the inquiry, asked him: "In your view, were there deficiencies in News International's systems for identifying and assessing legal risk, particularly in the context of potential reputational harm for the company?"
Former Formula One chief Max Mosley
Murdoch said: "With respect to news-gathering processes, for example, one of the subjects of interest here, I think it's self-evident that in hindsight, knowing what we know now, whatever controls were in place failed to create the sufficient transparency around those issues and the risks around it ...
"At the time I didn't have a view that those were insufficient or not."
Mosley was awarded a record £60,000 in privacy damages at the High Court over the March 2008 News of the World story about his sex life.
Murdoch agreed that News International also had to pay "substantial" costs, which he said was a "cause for concern".
"The story shouldn't have been run," he told the inquiry.
Campaigners from Avaaz protest dressed as Rupert Murdoch and his son James Murdoch outside the Royal Courts of Justice
The News of the World was closed down last July after revelations that it listened to the voicemails of murdered schoolgirl Milly Dowler.
Murdoch said the Sunday tabloid - Britain's top-selling paper - "had a connection with its readers" and was popular with them and with advertisers.
But he added: "In the end the profitability of the News of the World did not save it."
Murdoch told the inquiry he had been given "assurances" that measures were put in place to ensure journalistic standards were met.
"I was assured that from a standpoint of journalistic ethics and things like the Editors' Code and the PCC Code that extensive training had gone on and was continually going on and I was given strong assurances that this had happened."
But he said ethical and legal risks at the News of the World were "very much in the hands of the editor", and he was "not in the business of deciding what to put in newspapers".
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Asked about phone hacking at the now-defunct tabloid, Mr Murdoch said he stood by his evidence given to the Culture, Media and Sport Committee in July and November last year, saying he had not seen the now-notorious "For Neville" email.
"That remains my position, I stand by that testimony," he said.
He said he had been assured by former editor Colin Myler and then human resources director Daniel Cloke that hacking was not widespread.
Asked by counsel for the inquiry Robert Jay QC if he knew the problem was more extensive than just one reporter, Murdoch said: "No, to the contrary.
The assurances that I was given were the same assurances that were given to the Select Committee - that the paper had been investigated thoroughly, no new evidence was found, that the police had closed the case and had made public announcements to that effect."
He said he had a "general awareness that a reporter had illegally intercepted voicemails, had gone to jail along with the private investigator involved".
"It was a general understanding of an event in the past."
Rupert Murdoch is due to give evidence before the inquiry on Wednesday.