An air charter company has confirmed one of its light planes crashed just before midday on Tuesday, with fears held for the pilot.
Air Frontier said its twin-engined Beechcraft Baron aircraft went missing after taking off from Gove airport at Nhulunbuy on the Northern Territory coast with only the pilot aboard.
It was due to land at the remote Indigenous community of Numbulwar at 11.50am but never arrived.
A search led by NT Police began after a witness on a vessel reported seeing the plane crash into the sea near Isle Woodah.
In a statement on Tuesday evening police said no aircraft wreckage or persons had yet been located.
Search operations were suspended about 9pm on Tuesday and resumed at 6.30am on Wednesday involving police and Aboriginal rangers vessels, a helicopter and a police plane.
Police divers were also being deployed to conduct searches of the sea floor in the vicinity of the crash site.
"Divers will work to locate and recover aircraft debris and other evidence that may assist in establishing the circumstances of the crash," police said in a statement early on Wednesday.
Air Frontier CEO Kylie Hunt said the aircraft was undertaking a repositioning flight with no passengers aboard.
"Air Frontier is deeply saddened by this accident and our thoughts are with our pilot and their family at this incredibly difficult time," she said in a statement.
As a precautionary measure, the company had grounded all five of its Beechcraft Baron aircraft pending advice from authorities.
"As is standard process, the cause of the accident will be a matter for the investigating authorities and it would be inappropriate to speculate at this time," Ms Hunt said.
An Australian Maritime Safety Authority search and rescue jet out of Cairns circled the crash area on Tuesday afternoon.
CareFlight aircraft also took part in the search into the evening.
The Australian Transport Safety Bureau has been notified of the crash and has initiated an investigation.
Search Mission Co-ordinator, Acting Sergeant Nathan Conelius, said police remained focused on the search and supporting those affected.
"Our focus remains locating the pilot of the aircraft and alongside our partner agencies, we will continue search efforts," he said.
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