Earlier today, it emerged that the Metropolitan Police is investigating the Rupert Murdoch-owned newspaper after claims that one of its journalists hacked into the email of an anonymous blogger known as Nightjack.
Labour MP Tom Watson said that the Met Police had launched the probe after he submitted an official complaint.
He tweeted: "The Met police have confirmed to me they are investigating @rupertmurdoch's newspaper The Times over email hacking."
Last month, Harding told the Leveson inquiry into press ethics and standards that a former reporter at the paper had been 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."
It is thought 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 disclosing the life of a serving policeman was shut down after he was "outed" by The Times in a June 2009 article.
The article claimed that Foster "deduced" the identity of Nightjack. He was later dismissed from the paper "following an unrelated incident", and has since worked freelance for The Guardian and The Daily Telegraph.
In a further letter to the inquiry, Harding said: "When the reporter informed his managers that, in the course of his investigation, he had on his own initiative sought unauthorised access to an email account, he was told that if he wanted to pursue the story he had to use legitimate means to do so.
"He did, identifying the person at the heart of the story using his own sources and information publicly available on the internet.
"On that basis we made the case in the High Court that the newspaper should be allowed to publish in the public interest. After the judge ruled that we could publish in the public interest, we did."
But Watson wrote to the police on January 23, asking them to investigate the matter after Harding's admission that a reporter had tried to access a private email account.
The MP has now published a letter, sent to him by detective superintendent John Levett, on his website, which says: "I write to reassure you that the concerns raised within your letters are under investigation and officers from Operation Tuleta are dealing directly with the victim."
It is also understood that The Sun editor Dominic Mohan is to be recalled to Leveson, although it is unclear whether this is in relation to recent arrests at the paper.