The Department of the Prime Minister says it will not release emails from Malcolm Turnbull’s private email server, arguing it “does not have access to or provide administration support” for personal email servers and holds no records in its possession.

In October the Australian reported that Turnbull had been operating a separate email server outside the parliamentary email system, provoking questions over both the security implications and the potentially limited public access to the records under freedom of information and archive laws.

Use of the private server resonated because of the recent concerns over Hillary Clinton’s use of a private email server during her time as US secretary of state. Her private emails are now being periodically released by the State Department.

After Labor leader Bill Shorten questioned whether it was being used to avoid public scrutiny, Turnbull defended his use of the server. At the time a spokesman said all communications “which relate to his or her duties are ... potentially subject to [freedom of information] whether it is on SMS, a private email server or a government email server”.

When Guardian Australia requested access to correspondence from the private server across September and October 2015 relating to Turnbull’s official business, the prime minister’s department refused the request on the grounds that it held no documents in its possession within the scope of the request.

First assistant secretary Pip Spence wrote in the freedom of information decision letter: “The department does not have access to or provide administration support for personal email servers and does not hold any documents received from such a server. I have therefore decided to refuse the request.”

She drew attention to a letter tabled in Senate estimates by Allan McKinnon, the deputy secretary of national security, relating to the use of alternative systems of communication, following a request for advice from Turnbull.

In McKinnon’s response tabled in the Senate he wrote that information may be conveyed on a range of devices where the information is unclassified or not sensitive.

“Any documents in your possession that relate to your ministerial duties are subject to the Freedom of Information Act 1982 regardless of what system they are held in. The FOI Act does not apply to documents of a party political nature, documents held in your capacity as a local member, or your personal documents,” he wrote.

But the response from Turnbull’s department highlights one of the limitations of Australia’s freedom of information laws.

Had Turnbull’s private email server been managed by the department – as normally occurs with government emails – it would have been accessible by it and subject to Guardian Australia’s freedom of information request.

The department is also under no obligation to request access to the emails from the prime minister or the private company he has contracted for the purposes of processing the request.

Government agencies are only required to request documents from private entities when it relates to the performance of a commonwealth contract. It is unclear whether the prime minister’s arrangement with the email server could be characterised in this way.

A separate freedom of information request to the prime minister’s office is pending. But the prime minister’s department made no move to transfer the request directly to Turnbull’s office.

Under freedom of information laws government agencies are obliged to transfer requests to another agency when they believe documents are, to their knowledge, in possession of another government department.

The prime minister’s office has been contacted for comment.