The Minister told the Australian Federal Police Association that AFP protective service officers guarding military bases would be replaced by private security guards because a risk assessment had found there was less threat of an attack.

His letter to the association appears to contradict previous advice by the AFP saying protective service officers would be replaced because of budget cuts.

''Who is telling the truth and who is not?'' Federal Police Association national president Jon Hunt-Sharman said.

''The past 15 years has shown the threat to soldiers will not end with their duty abroad - there has been a 15-year trend of Islamist militants trying to kill Western soldiers on home soil.''

Armed guards from the AFP were brought in to protect military bases after the foiled terrorist plot at Sydney's Holsworthy Barracks in 2009.

The Australian Security Intelligence Organisation assesses the terrorist threat to Australia while the security assessment for bases was done by Defence security specialists in conjunction with Defence intelligence and military personnel.

A Defence spokesperson said the AFP was advised about the security risk assessment.

Senator Johnston in his November 1 letter to the Federal Police Association said decisions regarding base security were always based on intelligence-led risk assessments.

''The changes to AFP Protective Service manning are commensurate with the security risk and Defence is working closely with the AFP leadership to ensure this remains the case,'' he wrote.

''While the Defence proposal reflects a reduction at some locations and an increase at one establishment, all locations serviced by AFP protective service officers will retain an effective security presence.''

Australian Defence Association executive director Neil James said the push to reduce security came from the Defence Reform Program initiated by the Rudd government.

''It's essentially a bureaucracy-led budgetary measure rather than a politically initiated one, except that governments of all political persuasions insist on cuts to Defence's non-front-line functions, and where short-term fiscal goals and supposed financial efficiency often comes at the price of actual operational - and perhaps financial - efficiency,'' he said.

Mr Hunt-Sharman said it was appalling the government was replacing AFP protective service officers with security guards who patrolled shopping centres.

''They are not trained, qualified or experienced to protect high-threat terrorist targets,'' he said.

An AFP spokeswoman said any staff affected by the changes would be moved into sworn policing or into other roles in the broader AFP.