The vaccination of chickens against avian flu could lead to new strains which are a greater danger to humans.
Many chickens are being vaccinated
China and Indonesia are among countries vaccinating millions of birds against the virus.
But experts have said the flu virus may now mutate in vaccinated chickens into a form that could spread from person to person, New Scientist magazine reports.
The World Health Organization (WHO) said vaccination remained one important way of fighting the flu outbreak.
By mid-March, the WHO had reported 12 confirmed cases in Thailand alone, eight of them fatal.
The current form of H5N1 bird flu can spread from birds to humans, but not from person to person.
But scientists warned the virus is probably still circulating among vaccinated birds and could evolve into a form which can spread by human to human contact.
This is because flu vaccines are not 100% effective and some viruses can replicate in animals' or birds' bodies and continue to spread in "silent epidemics".
Ilaria Capua, of the World Organisation for Animal Health, and Richard Webby at St Jude Children's Research Hospital in Memphis, Tennessee, told New Scientist that without close surveillance vaccinations run the danger of spreading a virus.
A study by the US Department of Agriculture's poultry research lab in Georgia, to be published in the Journal of Virology, found evidence that following an outbreak in Mexico in 1995 of another form of flu, H5N2, different strains developed in vaccinated chickens.
These new forms are increasingly different to the vaccine strain, meaning affected birds will spread the infection more readily.
It is usually seen as preferable to slaughter affected birds and animals than vaccinate.
A WHO spokesman backed the current policy for tackling avian flu. He said: "Our goal is to reduce the threat to human health. The primary means of doing that is culling all infected birds, but vaccination does have a role to play."
He said the danger of the virus mutating to a form which could pass from human to human as a result of vaccination was a "theoretical" one and said this risk had to be weighed against the danger currently posed to humans.
Dr Maria Zambon, of the Health Protection Agency, said:
"Drastic measures are required to reduce avian influenza in poultry, which should in turn reduce the risk of transmission of avian influenza to humans.
"Control measures may include culling poultry flocks, improving hygiene and vaccination. The economic impact of repeated culling may be disastrous and other measures need to be considered seriously.
"Vaccination is one such approach which has proven to be useful in other countries and it is likely that it will help to reduce the burden of disease in poultry in south-east Asia. The success of any vaccination campaign will depend on the proportion of chickens vaccinated."