The broadcaster revealed a member of staff was cleared to carry out the hacking, a breach of the Computer Misuse Act, on two separate occasions that it believed were "in the public interest".
Gerard Tubb, the broadcaster's northern England correspondent, accessed the emails when Darwin's wife, Anne, was due to stand trial for deception in July 2008.
He also accessed the email accounts of a suspected paedeophile in an investigation that did not lead to any material being published or broadcast. Both instances of hacking were approved by Simon Cole, the managing editor of Sky News, it was reported.
Sky is part-owned by Rupert Murdoch's News Corporation. The broadcaster's parent company, BSkyB, is currently being investigated by the communications regulator, Ofcom, in the wake of the News of the World phone-hacking scandal.
James Murdoch, the former executive chairman of News International, stepped down as News Corporation's chairman on Wednesday.
Yesterday, John Ryley, the head of Sky News, said in a statement that the broadcaster had "authorised a journalist to access the emails of individuals suspected of criminal activity" and the hacking in both cases was "justified and in the public interest".
Mr Ryley claimed the broadcaster's decisions required "finely balanced judgment" and they were "subjected to the proper editorial controls".
Darwin, from Seaton Carew, near Hartlepool, was declared dead after vanishing at sea in his canoe in March 2002. His wife later cashed in his insurance and pension schemes and moved to Panama.
The couple's conspiracy was exposed in 2007 after Darwin turned up at a London police station claiming to be a missing person and suffering from amnesia. He pleaded guilty to seven charges of deception while his wife faced six charges of deception and nine of money laundering.
Darwin was sentenced to six years and three months in prison and was released on licence from Moorland open prison in Doncaster, in January last year. His wife received six and a half years and was freed in March 2011.
Sky News said Mr Tubb had discovered that John Darwin used the identity of a friend, John Jones.
According to the broadcaster, Mr Tubb then discovered a Yahoo email account in the name John Jones and later sought permission to access the emails.
Shortly after, Mr Tubb produced a story for Sky's news channel and website in which he quoted from emails which had been written by Darwin to his wife and to a lawyer.
The basis of the story was that Darwin was being forced to return to Britain as changes to visa regulations meant he could no longer stay in Panama.
Intercepting emails is an offence under the Computer Misuse Act, and there is no public interest defence written in law.
In a statement, Mr Ryley said: "Sky News is committed to the highest editorial standards. Like other news organisations, we are acutely aware of the tensions that can arise between the law and responsible investigative journalism.
"On two occasions, we have authorised a journalist to access the email of individuals suspected of criminal activity. In the 2008 case of Anne Darwin, Sky News met with Cleveland Police and provided them with emails offering new information relevant to Mrs Darwin's defence. Material provided by Sky News was used in the successful prosecution and the police made clear after the trial that this information was pivotal to the case.
"We stand by these actions as editorially justified and in the public interest. We do not take such decisions lightly or frequently."
