While the mission to train Afghan army and police in the Uruzgan province will take two to four years, diggers will remain there past that time, he said.
"We will still be there supporting them beyond the two to four years, for a period of time," Air Chief Marshal Houston told ABC Radio on Thursday.
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Houston says he is aware of polls showing a large number of people are concerned about Australia's involvement in Afghanistan.
"But there's also a large number who think it's very necessary that we continue to run this contribution to the counter-insurgency campaign."
The mission was well defined and Australian troops were performing "superbly" despite the losses.
Air Chief Marshal Houston said young Afghan soldiers were improving day by day.
"I know by the end of the training period they will be a very good fighting formation.
That will be the legacy we leave."
Air Chief Marshal Houston criticised retired Australian general Jim Molan, who has questioned the strategy and troop numbers on the ground in Afghanistan.
"It's very dangerous for people in Canberra to be talking about circumstances on the ground when even I do not have all of the details," he said.
General Molan said Australia had been refusing to examine the option of increasing the troops and devoting more resources to the conflict.
