The last federal police officers engaged in Australia's first and longest-running peacekeeping mission have withdrawn from Cyprus.

A flag-lowering ceremony at the Cypriot capital's defunct airport that serves as the UN force's headquarters overnight drew the curtains on Australia's 53 year mission, with the three officers officially pulling out.

"While the AFP is leaving Cyprus, the mark of its officers will remain enduring," Justice Minister Michael Keenan told AAP.

"Over the past five decades the AFP has provided security and stability to a community facing challenging circumstances."

AFP commissioner Andrew Colvin described the withdrawal from Cyprus as a sad but proud day.

More than 1600 Australian officers have contributed to the United Nations Peacekeeping Force in Cyprus since 1964.

It was the first time the UN deployed civilian police in a peacekeeping mission to bring an end to hostilities in a troubled nation.

The first Australian contingent of 40 police officers arrived in Cyprus in May 1964. Since then, 111 Australian contingents have served with the peacekeeping force.

Three Australian officers died while serving in Cyprus.

Officers worked in the UN-established buffer zone to maintain peace and stability, delivering humanitarian assistance to isolated residents and performing a liaison role between authorities from the north and south.

"The AFP not only earned the trust of the community, but their respect and gratitude," Mr Keenan said.

"For the AFP, the experience gained from its first peacekeeping mission has been invaluable, and will continue to be drawn upon for ongoing missions across the world."