Prime Minister Tony Abbott is expected to announce on Tuesday that the final legal hurdles with the Iraqi government have been cleared, meaning the Australian commandos can begin their ''advise and assist'' work with the Iraqis.

The paperwork from Baghdad came as RAAF Super Hornet fighters returned safely to the United Arab Emirates from their first combat mission in Iraq, providing air cover for local troops in the country's north, though they did not fire weapons.

But even as the RAAF missions began, Defence Minister David Johnston acknowledged that the Islamic State fighters were quickly adapting to air strikes.

''I think that's pretty certain that they will adapt very quickly not to be out in the open where the Iraqi security forces can call in an air strike,'' he said.

Air strikes against fixed targets would be less frequent but would rather be in support of Iraqi and Kurdish forces on the ground, he said, as the US was doing in the besieged northern Syrian town of Kobani.

Senator Johnston acknowledged this would be harder in the major Islamic State strongholds in Iraq such as Fallujah, Ramadi and Tikrit, where the Iraqi forces would need to drive the militants out. ''I think it was always going to be … that the Iraqi security forces would have to step up and go into these towns and clean them out.''

The former Chief of Air Force, retired Air Marshal Geoff Shepherd, said the militants would ''melt'' back into the population.

''At the start of their campaigns, they were massing as a military force … but they're smart enough now to melt back into the population and it will be more difficult to contain them by air power alone.''

He warned that this could raise the risk of civilian casualties,

which would need to be avoided so as not to lose the ''hearts and minds'' campaign. ''We're not going to win this just by bombing. We're going to win it by challenging their ideology and their view of the world, and every time we kill an innocent civilian … that drives people into the arms of jihadis.''

In what could be a grim portent of things to come, Syrian Kurds warned that air strikes were failing to halt the advance of the Islamic State in that country's north as they lay siege to Kobani, a key town near the border with Turkey.

Up to 200 Australian special forces soldiers will work in Iraq, bolstering the local troops on the ground.

It is understood that some have already left Al Minhad Air Base in the United Arab Emirates before the final legal clearance to begin work.

Their focus will be on strengthening the leadership ranks among the Iraqis to avoid the military collapses that allowed the Islamic State to seize large swathes of territory in recent months.

But Fairfax Media understands that among the troops will also be elite joint terminal attack controllers - special forces experts who can call in air strikes from the ground with great accuracy.

They would work with the RAAF Super Hornets and Wedgetail surveillance and control planes to hit moving Islamic State targets while the Iraqi army fights them on the ground.

The Abbott government needed a detailed legal agreement with the new government in Baghdad that ensures Australian Defence Force personnel have the necessary legal cover if, for instance, they are involved in the deaths of civilians.