Mr Stokes and his family were not on board at the time, and have stayed in Madang to continue their scuba diving holiday off the east coast of Papua New Guinea.
Mr Stokes' 36-metre luxury motor yacht Antipodean arrived from Cairns on Wednesday, and was anchored off Kranget Island, near Madang, on Thursday.
"In the early hours they were boarded by armed pirates and robbed," said former Madang Governor and owner of the Madang Resort Hotel, Sir Peter Barter.
In an email obtained by the ABC, Sir Peter said the thieves stole watches, mobile phones, laptops, diving equipment and cash.
However, a spokeswoman for the Stokes family who had spoken with the crew said only food and diving equipment was taken.
She said three locals armed with long 'bushknives' boarded the vessel and were confronted by the Papua New Guinean crew.
The thieves left in their own boat after the confrontation and there were no reports of injuries.
The billionaire boss of Channel Seven flew into Madang with his family on Sunday.
The spokeswoman said the Stokes family had visited Madang several times, and had good relations with the local community.
"They did not want to make an issue over this incident, but we insisted that a report was made to police," Sir Peter said.
"Regretfully, this incident is already known around Cairns and will deter motor yachts [and] tourists from visiting Madang and PNG."
Papua New Guinea’s Minister for Tourism was expected to release a statement about the incident on Tuesday, but did not.
Madang police are reported to be investigating but could not be reached for comment.
The armed robbery is the latest blow to Papua New Guinea’s tourism industry.
A year ago, local villagers armed with machetes, spears and guns attacked a trekking group on the Black Cat track in Morobe province, killing three Papua New Guinean porters and injuring several of the Australian and New Zealand hikers.