In a highly unusual move, the Australian Federal Police representative has been removed from the office of Home Affairs Minister Peter Dutton.

Both the minister and the AFP are playing down the decision but 9NEWS has been told it is the first time since the mid-1990s that the federal police have not had an officer placed with the relevant minister in Parliament House.

Government agencies commonly have Departmental Liaison Officers embedded with ministers to act as a bridge to the department and 9NEWS has confirmed the AFP representative left Parliament months ago.

Home Affairs is now a super-portfolio that combines immigration, border protection, law enforcement and Australia’s domestic spy agency ASIO.

The representative left the office of Mr Dutton months ago. (AAP)

A statement from the minister says the liaison officers are drawn from across the portfolio.

“Given the number of agencies within (Home Affairs) it is not possible for all agencies to have a DLO in the Minister’s office at any given time,” the statement said.

This seems at odds with the entire reason for establishing the super-portfolio, which was to give it complete oversight of every agency involved in domestic security.

Not including the police could be seen as downgrading the role of the frontline law enforcement agency.