Department for Education staff repeatedly destroyed official government correspondence, it has been reported.
According to the Financial Times (FT) around 130 emails sent to and from the account of special adviser Henry de Zoete were deleted.
The alleged practice was uncovered by journalistic ethics charity the Media Standards Trust.
Michael 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.
Mr 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 Department for Education 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."
On Friday Mr Gove lost the latest round in his freedom of information battle to keep details of emails from his personal account secret.
Information Commissioner Christopher Graham ruled that the emails were covered by the Freedom of Information Act because 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.
Reports last September suggested that Mr Gove had been using a private email account named "Mrs Blurt" rather than his departmental account to discuss government business with advisers.
Mr 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 Mr 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."
Labour MP Tom Watson, who sits on the Culture, Media and Sport Select Committee, said: "It's quite right that the Information Commissioner has ordered Michael Gove's emails, sent from his wife's account on what appears to be official business, to be disclosed to the Financial Times under their FOI request.
"The public want to know more details of the nature of this government business and why he had to use a private email to carry it out.
"To date, the first class journalism of the FT has revealed that Michael Gove's special adviser Henry de Zoete has deleted about 130 emails relating to key departmental issues.
"I hope, according to rules laid down by the Lord Chancellor, that the correct deletion logs are available, so the public will be able to have a better understanding of why important official emails have disappeared.
"If not, this will add to a growing sense that there's a somewhat impenetrable cloud of obfuscation cloaking Michael Gove's Department for Education."