The World Health Organisation has expressed concern Indonesia has stopped sharing information about bird flu ahead of a vaccine deal with a US firm.
More than 60 people have died from H5N1 in Indonesia
A senior WHO official, David Heymann, said Indonesia had not shared bird flu samples since the start of the year.
A health ministry spokesman in Jakarta said the deal with Baxter International this week was to protect locals.
The current outbreak of the H5N1 bird flu has killed more than 60 people in Indonesia over the past two years.
The deal with Baxter International is expected to be announced on Wednesday.
There was no immediate comment from the US firm.
The samples are vital in keeping track of the small genetic mutations the virus undergoes, as scientists watch for the emergence of a strain that could cause a serious human flu epidemic.
Dr Heymann said the move called into question 50 years of global co-operation - what he called a cornerstone of the fight against influenza, the BBC's Chris Xia said.
Keeping poultry in backyards has been banned
Indonesian officials also say that they want to maintain intellectual property rights over the strains of the H5N1 virus that are discovered in the country.
"We cannot share (virus) samples for free. There should be rules of the game for it," a health ministry spokeswoman was quoted by news agency Reuters.
WHO has acknowledged that in the past vaccines have been produced using genetic material from poor countries, but the benefits have not been evenly spread and have mostly gone to developed countries.
Experts fear that by cutting such an exclusive commercial deal, Indonesia could be working against the greater public interest in tackling the global spread of the flu strain, our correspondent said.
Mr Heymann told Reuters the WHO had been working with Indonesian authorities over the issue and would continue talks with them and with drug companies.
Indonesia has recently banned keeping poultry in back yards amid fears of more flu outbreaks.