Prime Minister Tony Abbott will leave Arnhem Land to farewell Australian troops bound for Iraq.

Just hours before touching down in the region at the weekend, Mr Abbott announced the deployment of 600 troops to help combat Islamic State.

He had indicated he may cut his week-long trip short to deal with security issues. Mr Abbott’s office has now confirmed he will now fly out of Nhulunbuy on Thursday.

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However, the prime minister remains committed to fulfilling his promise to spend a week in indigenous communities so will return to Arnhem Land on Friday.

AAP understands Mr Abbott is considering visiting one of two bases to farewell troops – one being the Amberley RAAF base near Brisbane, where Super Hornet fighter jets are based.

The prime minister has been running the government with the help of several ministers from a temporary tent village in the area.

He will spend Wednesday with school attendance officers and teachers at a local school before meeting with his indigenous advisory council.