AFP Commissioner Tony Negus quits

Commissioner Negus knocked back a chance to serve another term in the role and advised the federal government that he would finish as head of the AFP at the end of his five-year appointment on September 7.

The government will now launch an extensive national and international search to find a new AFP boss.

In a statement posted on the AFP webpage, Commissioner Negus is quoted as saying it was a privilege to serve the Australian community.

''During this time the AFP has achieved record levels of performance across the board and the organisation is well placed to continue to build on these accomplishments,'' the statement read.

''I am also very proud of the domestic and international relationships that the AFP has developed during my term, with co-operation in fighting both terrorism and transnational crime at an all-time high.''

Commissioner Negus spoke at a ceremony to welcome 28 new probationary constables to the ranks of the AFP on Friday. He declined to be interviewed about his departure.

Justice Minister Michael Keenan congratulated the departing chief for a ''long and distinguished law enforcement career ... serving both Australia and the region''.

''Under Commissioner Negus' leadership and reforms, the AFP has consistently achieved record levels of success in the protection of our nation,'' a statement from the minister said.

''The AFP has also successfully undertaken a range of international deployments contributing to international peace and stability during this time, including Afghanistan, Papua New Guinea and the Solomon Islands.''

In June 2005 Commissioner Negus was named in the Queen's Birthday honours list and awarded the Australian Police Medal.

He also received the recipient of several international awards, including Indonesia's highest level of police recognition, the Bintang Bhayangkara Utama medal, the US 911 medal and the Interpol Safer World medal in recognition of his significant contribution to global safety and security.

But his time at the top also attracted some controversy.

Commissioner Negus came under fire earlier this year after allegations his son, Mitchell, had been given special treatment when he was allowed to graduate from the AFP while injured and under investigation for a motorcycle crash.

There is no suggestion his resignation is linked to the allegations.

The Canberra Times revealed in February Mitchell Negus had quit the force shortly after he became embroiled in an internal AFP inquiry and an investigation by local police looking at speeding in the crash.

Commissioner Negus sat in on his post-accident interview with local officers, something said to have been done ''as his father''.

The AFP denied that the commissioner played any role in the internal investigation.

In 2011, Commissioner Negus was forced to deflect questions about his relationship with an assistant he took on overseas business trips.

AFP Association national president Jon Hunt-Sharman said his members had been surprised Commissioner Negus would not continue in the role.

Commissioner Negus broke the news to AFP employees via an all staff message on Friday. The two previous AFP Commissioners, Mick Keelty and Mick Palmer, were both offered and accepted second terms as AFP Commissioner.

Mr Hunt-Sharman said the AFPA believed the next commissioner should have extensive AFP national and international operational experience, along with a community policing background.

He said the AFPA believed Deputy Commissioner Mike Phelan and Deputy Commissioner Andrew Colvin were qualified to lead the AFP into the future, should either of them apply for the vacant position.

"It is important that our next Commissioner not just has extensive experience in the unique operational environment of the AFP locally, nationally and internationally, but that they also are well traversed in modern management practices that support the employment needs of the current generation of employees who value work life balance, fairness and transparency, and shared decision making."