The dispute adds to mounting opposition to Phoenix Life Sciences International, which claims its drug can treat diabetes.
Phoenix Life has wasted no time since obtaining approval from Vanuatu's government to manufacture drugs last October.
In March, it broke ground on a clinic and pharmacy in Port Vila and recruited a former Health Ministry director general.
But its diabetes-treating drug has prompted scepticism from health experts and Vanuatu's doctors' association, who want an ethics committee formed.
And in its annual report released on Friday, Phoenix Life said it was involved in two disputes in Vanuatu over deposits due on proposed property purchases.
The company said it was confident it will win bids to dismiss both claims.
Its CEO Martin Tindall also said its research projects would comply with Australian and Vanuatu ethics committee guidelines
"The attorneys representing the company in Vanuatu maintain that the claims are spurious, as the related contracts were never validly executed and at no time were unconditional, negating any obligation by the company to pay the deposit."
The President of the Vanuatu Medical and Dental Association, Dr Basil Leodoro, told the Vanuatu Daily Post last week that he did not support the proposed cannabis drug trials on people with diabetes.
"There is no hard evidence today that shows that marijuana can treat diabetes," he said.
Writing on Facebook on Sunday, Phoenix Life chief executive Martin Tindall said the company took the need for scientific evidence into medicinal cannabis "very seriously."
He said any of the company's research projects would comply with Australian and Vanuatu ethics committee guidelines.
"Poorer countries such as Vanuatu are often ignored in the conduct of medical research in favour of conduct of research in more wealthy countries.
"It is very important that research is conducted in countries where the local medical and environmental conditions can be taken into account."