James Harding, who was appointed editor of The Times in 2007, told the inquiry into press ethics and standards that the News International paper has "never used or commissioned anyone who used computer hacking to source stories".
However, he admitted that a reporter was given a written warning for accessing a Hotmail email account, believed to be for the story on Nightjack.
In his written statement, Harding said: "There was an incident where the newsroom was concerned that a reporter had gained unauthorised access to an email account.
"When it was brought to my attention, the journalist faced disciplinary action. The reporter believed he was seeking to gain information in the public interest but we took the view he had fallen short of what was expected of a Times journalist. He was issued with a formal written warning for professional misconduct."
According to The Guardian, sources within The Times say that the reporter was graduate trainee Patrick Foster, who had correctly guessed answers to security questions for the anonymous Hotmail account operated by Lancashire police detective Richard Horton.
Horton's blog won the prestigious Orwell prize for revealing details of the life of a serving policeman, but was closed down after he was "outed" by The Times in a June 2009 article.
Harding's statement did not disclose the identity of the hacker or confirm that it had led to the publishing of the article, which claimed Foster had "deduced" the identity of Nightjack.
Also at the Leveson inquiry, News International chief executive Tom Mockridge said that Foster had subsequently been "dismissed following an unrelated incident".
The reporter, who is thought to have denied the unauthorised access, has since written freelance articles for The Guardian and The Daily Telegraph.
Elsewhere at the inquiry yesterday, long running Private Eye editor Ian Hislop criticised the cosy relationship between Rupert Murdoch's newspapers and politicians, along with the police.
The Have I Got News For You panellist said: "There are reasons [the Murdoch-owned] News International thought it could get away with whatever it liked... the Murdoch family was deeply embedded in our political top class."
However, he said that new laws specifically to govern the press were not needed because practices such as phone hacking and bribing police officers already contravene existing laws.
Instead, he called on the inquiry to ask why police and senior politicians were reluctant to uphold the law and stop newspapers from acting in such a way.
More Leveson coverage:
> Gordon Brown denies threatening to destroy Rupert Murdoch
> Daily Mirror phone hacking possibly hidden, admits editor
> Richard Desmond: Express vilified over McCanns coverage
> Daily Mail receives 400 Pippa Middleton pictures a day
> Hugh Grant suspects Mail on Sunday phone hacking
> The Daily Telegraph paid source £150k for MPs' expenses story
> Charlotte Church offered coverage deal to sing at Murdoch wedding