The Australian Defence Force jet carrying the Prince of Wales touched down at Townsville's RAAF Base at 11am, (AEST) after leaving New Zealand on Saturday morning.
He will travel by Blackhawk helicopter to the Cassowary Coast towns of Cardwell and Tully before heading north to Cairns.
Along the way he will meet volunteers who have helped residents recover in the wake of Cyclone Yasi which tore through north Queensland in early February.
Australian customs officials ventured aboard the plane to process the Prince and his entourage.The Prince emerged from the aircraft and was greeted by a line of dignitaries on the tarmac including Queensland Premier Anna Bligh, head of Queensland Recovery Taskforce Major General Mick Slater and federal Attorney-General Robert McClelland.
The "disaster tour", as some British media have dubbed it, also Takes Prince William in flood-damaged communities in southeast Queensland on Sunday and northwestern Victoria on Monday.
Queensland Premier Anna Bligh has said she hopes the royal visit will boost her state's struggling tourism industry.
"I hope he sends the message back to his friends and colleagues in the UK that Queensland is open for business, and that while he's here he gets an opportunity to see that for himself," she said before his visit.
The trip follows a similarly grim two-day tour of New Zealand, where the prince attended Christchurch's memorial service to remember the 182 who died in the February 22 earthquake.
Prince William also took the opportunity to visit families of the 29 men, including two Australians, killed in the Pike River Mine collapse in Greymouth last November.
The Prince will fly back to London to continue with plans for his impending wedding. He will marry long-time girlfriend Catherine Middleton at Westminster Abbey on April 29.
