On Tuesday afternoon Minister for Police and Emergency Services Mick Gentleman announced Ms Saunders had informed him of her decision.

Ms Saunders will join Mandy Newton as a deputy commissioner for the Australian Border Force under the command of commissioner Michael Outram.

Mr Gentleman thanked Ms Saunders for her work.

"Assistant commissioner Saunders brought with her a breadth of experience," Mr Gentleman said in a statement.

"Over her career, assistant commissioner Saunders spent more than 29 years working in community policing and national operational areas within the AFP, including drug importation and fraud."

He said he had worked closely with Ms Saunders since she took on the role of chief police officer.

"I have found her expertise and advice over this time invaluable. Her work with ACT Policing is to be commended.

"She has invested significant resources in engaging with the local community about policing matters. She has begun the important process of reforming the future of ACT Policing.

"She has also delivered strong results in combating the criminal activities of outlaw motor cycle gangs through Taskforce Nemesis."

Ms Saunders joined the AFP in 1989. She was named as ACT chief police officer in August 2016, replacing Rudi Lammers, and began in the position in November 2016.

Ms Newton, who is currently in the role of deputy commissioner support, will start in the role of deputy commissioner operations taking over from Clive Murray on September 3.

Ms Saunders will take over from Ms Newton as deputy commissioner support on October 29.

Commissioner Outram said both officers demonstrated extensive leadership and operational experience that would be essential in their respective new roles.

"Mandy and Justine bring further quality and strength to our renewed ABF senior leadership team and I congratulate them on their appointment following a highly competitive recruitment process," Commissioner Outram said.

"They will be instrumental in delivery on the ABF’s new vision and mission, guiding our values and behaviours, and improving our training, tradecraft and leadership across the agency.

"Their experience will help cement the ABF as a global leader in border law enforcement and a trusted partner that helps build a safe, secure and prosperous Australia."

President of the Australian Federal Police Association Angela Smith said the news did not come as a total surprise.

Ms Smith, who has reached out to Ms Saunders since the news broke, said she was sad to see Ms Saunders leaving.

"I think there’s far too much good talent leaving the AFP at the moment and I hope the AFP executives realises that," Ms Smith said.

"She’s a good operator and I think she’s tried her absolute best for ACT Policing in the short time she’s been there and I think she’s done an excellent job, probably more so than some previous chief officers and I think she’ll do really well in Border Force."

Requests were made for an interview with Ms Saunders.