"We maintain that (the virus sharing mechanism) has been misused for commercial purposes"
Dr Triono Soendoro, Indonesia's National Institute for Health Research and Development
Officials said the deal with Baxter was designed to ensure the country's 220 million people received access to a vaccine in the event of a human pandemic.
"We made the deal so we don't have to purchase the vaccines at market price," Dr Triono Soendoro, the head of Indonesia's National Institute for Health Research and Development told the Associated Press.
Under the agreement with Baxter other organisations, including the WHO, would only have access to Indonesian flu samples provided they agree not to pass them on to commercial vaccine makers.
"We maintain that (the virus sharing mechanism) has been misused for commercial purposes," said Soendoro.
Some experts sympathised with Indonesia but warned that the deal could jeopardise world-wide access to a pandemic vaccine.
Although the virus remains essentially an animal disease, experts fear it may mutate into a form which can jump species to humans and trigger a global pandemic.
Many fear that Indonesia will become the epicentre of a global outbreak.
Other countries including China, Thailand and Vietnam have previously stalled on the virus-sharing initiative for fear of rich countries stockpiling expensive vaccines and drugs and leave their populations vulnerable.