Michael Gove's staff at the Department for Education repeatedly destroyed official government correspondence, it was reported on Monday.
The alleged practice was uncovered by journalistic ethics charity the Media Standards Trust, an independent think tank that aims to raise standards in the press.
Martin Moore, director of the organisation, sought details of emails sent from Education Secretary Michael Gove's special advisers and a number of named journalists. The charity claimed that the Department for Education's response stated that the emails did not exist.
Moore told the FT: "Uncovering how the government spins its policies to the press is clearly in the public interest - especially now, during the Leveson Inquiry.
"If the Department for Education is destroying emails to frustrate that, it would be both shocking and wrong."
A DfE spokesman said: "Emails are not automatically considered an official record.
"Special advisers are not required to maintain records of deleted emails. All civil servants routinely delete or archive emails, taking account of their nature and content.
"Government systems could not operate if every civil servant kept every email they send or received. The act of deleting emails is not evidence of wrongdoing."
Information Commissioner Christopher Graham ruled that the Freedom of Information Act covered the emails as the messages dealt with departmental business.
He told the Department for Education either to release the information requested or issue a formal refusal notice setting out why it is being withheld.
The use of private emails to conduct departmental business was first revealed in August by The Huffington Post UK after an email was leaked showing Whitehall officials pressuring a school into becoming an academy.
Reports last September suggested that Gove had been using a private email account named "Mrs Blurt" rather than his departmental account to discuss government business with advisers.
Gove has been resisting the release of the information on the grounds that ministers' personal email accounts are not covered by the Act.
A spokesman for Graham's office said: "The Commissioner's decision is that the information amounted to departmental business and so was subject to freedom of information laws, being held on behalf of the Department for Education.
"The department is now required either to disclose the requested information - the subject line of the email and the date and time it was sent - or issue a refusal notice in accordance with the FOI Act giving reasons for withholding it."