The WHO’s statement on Thursday came as Indonesia and Pakistan bowed to international pressure to slaughter sick birds.
"If (the killing of birds) is done in such a way that exposes more people (to the virus), then this ... could be increasing the risk of developing a strain that you would not want to see," said WHO spokesman Dick Thompson.
The WHO has warned that while humans have so far only caught the disease through contact with infected birds or their droppings, it could claim millions of lives if it mutates into a form that can be passed among humans.
The warning came as Pakistan and Indonesia ordered a cull of sick chickens after insisting that the outbreaks of bird flu in their countries were not serious enough to warrant a mass
Countries across Asia have battled allegations of a cover-up, with China denying allegations on Thursday that it was the source of the bird flu outbreak which has hit 10 Asian nations so far.
"If (the killing of birds) is done in such a way that exposes more people (to the virus), then this ... could be increasing the risk of developing a strain that you would not want to see."
China became the latest Asian government to face charges of covering up the disease when the respected New Scientist journal in Britain said the epidemic probably erupted there as early as a year ago.
But as China halted poultry exports from its three affected provinces, the foreign ministry rejected the charges, and the WHO's Beijing-based spokesman Roy Wadia said it was too early to confirm China as the origin of the disease, which could have had several possible sources.
Proof of a cover-up would be extremely embarrassing for China which was strongly criticised last year after it emerged that authorities had hidden the outbreak of Severe Acute Respiratory Syndrome (SARS) for months.
Chinese Premier Wen Jiabao ordered local governments to implement an eight-point plan to control the flu outbreak, including intensified scientific research on the virus and the slaughter of all infected poultry, state media reported.
But amid the widening outbreak, Russia added China to its list of countries from which poultry imports are banned, and South Africa suspended shipments of chicken from the mainland.
The US government also warned Americans over the rapid spread of the bird flu in Asia, advising them to avoid live fowl and poultry markets.
In Thailand, the government also faced heavy flak after it admitted it had "screwed up" in its handling of the bird flu crisis which has now erupted in nearly half its 76 provinces and killed two children.
Pakistan has bowed to pressure
to slaughter birds
Indonesia, Laos and Vietnam have also faced charges of a cover-up that has allegedly hampered attempts to curb the spread of the disease which has led to the deaths or culling of more than 20 million poultry.
Indonesia on Thursday ordered the slaughter of all infected poultry after coming under pressure from the WHO, but it was unclear whether the cull would extend to healthy poultry as it has in other nations.
Georg Petersen, WHO representative in Indonesia, said the announcement was "very good news."
New Taiwan outbreak
Pakistan, the first South Asian country to detect bird flu, also on Thursday ordered the culling of all infected poultry but offered no compensation to induce farmers to kill their birds.
Taiwan reported new outbreaks in ducks and chickens at four farms in the south, and said that poultry there would be slaughtered.
In Vietnam, where eight people have died, bird flu has hit three more of Vietnam's 64 provinces and cities, taking the number affected to 31, the government said amid criticism that some areas were not tackling the disease properly.
The European Commission said it was sending an animal health expert to help fight the outbreak there in response to a call by the WHO for international assistance in tackling the spread of the disease.