Military personnel serving in Afghanistan are set to have their daily pay bonus cut after Defence assessed that the operation in the strife-torn country has entered a less dangerous phase.

And troops serving in the new Iraq campaign against Islamic State militants, who include special forces advisers and RAAF air crews, will receive the same lower allowance for so-called "warlike service" because Defence deems that work less risky than Afghanistan was at the height of the war there.

Lower allowances: The cut to Australian troops' pay is likely to be controversial.

The cut to the Afghanistan allowance is likely to be politically sensitive, following a recent contentious pay deal that will lift military personnel pay by less than inflation, meaning they will get a pay cut in real terms.

The daily bonus for personnel serving through the Afghanistan campaign, which included years of fierce combat and the loss of 41 Australian diggers' lives, has been $200 a day. That will continue up to December 31, though Australia's main base at Tarin Kowt closed down at the end of last year, leaving only about 400 troops mainly stationed in the capital Kabul in training and advisory roles.