A statement from the coalition said it had "immediately complied with all directions received from our Iraqi partners as they implemented the Prime Minister's order".

Prime Minister Adel Abdel Mahdi on Thursday said he was cancelling "special approvals" for aircraft operating in Iraqi airspace, which since 2014 have included coalition aircraft bombing the Islamic State group.

"The authorisations will come exclusively from the head of the armed forces," his office said.

The decision would apply to reconnaissance operations, fighter jets, helicopters and drones, and include "all Iraqi and non-Iraqi entities". It did not specifically mention flights operated by the coalition.

Any aircraft flying without the proper approvals "will be considered hostile aircraft and will be immediately handled by our air defences", according to Abdel Mahdi's instructions.

The coalition said Friday that its senior leaders had met with Iraqi defence officials to implement the decision and insisted it was operating "in Iraq at the request, and under the protection, of the Government of Iraq".

It came days after a mysterious explosion at an arms depot at the Saqr military camp south of Baghdad, which sent missiles stored there flying into neighbouring areas, wounding 29 people.

Abdel Mahdi's ordered an investigation into the incident to be submitted within a week and said all military bases and arms depots were to be moved outside Iraqi cities.

Following the US-led invasion that overthrew dictator Saddam Hussein in 2003, US troop numbers peaked at some 170,000 before a full withdrawal was completed in 2011.

Troops returned to Iraq in 2014 as part of an international coalition set up to fight the Islamic State group after it swept through much of the north and west, and several thousand are still thought to be based in Iraq.

The coalition was still carrying out rare air strikes against IS sleeper cells as of last month.