THE DAMAGED boat of a man missing near Nhulunbuy in east Arnhem Land has been found on the rocks of Cape Wilberforce this morning, police have said.

Superintendent Michael White said the ghost yacht "Roxanne" was found floating with nobody on it by a passing vessel about 35km from Gove, which itself is about 640km east of Darwin.

He said the missing 61-year-old man set off from the Gove Yacht Club about 7:30am yesterday.

"We believe the man was travelling to Darwin alone," he said in a media release.

"The hull appears to have been damaged causing the vessel to take on water."

Supt White said an emergency locator beacon or EPIRB may have been on the yacht but may not have been activated before it departed.

Police, NT Emergency Services and national civil search co-ordinators Australian Search and Rescue (AusSAR) are searching for the missing man by air.

Police have urged anyone passing near or over the area to keep an eye out for the man.

THE search for a missing yachtsman is still continuing off the Territory coast.

Bruce Edwards, 61, left Nhulunbuy for Darwin - 646km as the cocky flies - on Tuesday morning aboard his 10m steel yacht Roxanne.

The boat was found unmanned two days later, smashing on to rocks and taking on water at Cape Wilberforce, 35km northwest of Nhulunbuy.

Police searched between Nhulunbuy Harbour and No Name Bay at a "very low" altitude from a private Darwin-based R44 helicopter today.

They patrolled on foot and by boat on Friday.

The holed boat is still on the rocks because police have no means of removing it.

But Senior Sergeant Brendan Muldoon said officers are retrieving as many personal belongings from Roxanne at low tide as they can carry to give to Mr Edwards' family.

"We're confident we haven't missed him," he said.

"The water is crystal clear and we've had fantastic weather."