Mr Howard says Australia's presence in the region will continue, with any changes being made on the basis of security and safety.
The Australian troops in Al Muthanna were sent to guard a civilian and military reconstruction unit which had been sent by Japan.
The Prime Minister says even if the Japanese pull out this year, as expected, Australian troops will stay to be involved in training and other security matters.
Earlier this week, the Defence Minister, Brendan Nelson said Australia would extend its troop deployment in southern Iraq for another six months after Japan said its military engineers would stay on.
470 Australian troops are currently based at in the Al Muthanna province.