Pakistani officials say a strain of bird flu has been found in chickens in the southern port of Karachi.
The Pakistan poultry industry says it is unhappy with the cull
The government has recommended a cull of poultry in the area.
The influenza has been identified as H-7 and H-9, strains which are said to be less dangerous than H-5N1, which is afflicting South-East Asia.
An agriculture ministry official said there was no evidence that the strains found in Pakistan had spread to humans.
Since November, between 1.5 million and 3.5 million chickens have died in Sindh province, but authorities say only a few thousand were from avian flu.
Manzoor Panwar, minister for livestock in Sindh province, told the AFP news agency: "The large number [of dead] which has been reported by farmers can be linked to conventional diseases."
Nevertheless, a government circular sent to poultry farms read: "There is no solution to get rid of the said disease problem other than its eradication through destroying all birds."
Mr Panwar said vaccinations were being provided to prevent further outbreaks.
However, the poultry industry was unhappy with the government's response.
Pakistan Poultry Association convener Abdul Maroof Siddiqui told the AFP news agency: "We have very strong doubts over the government's ability to diagnose the disease as avian flu, as they do not have human or technical expertise."
Mr Siddiqui said there had been "widespread death" at poultry farms around Karachi but that researchers were unable to detect whether it was bird flu or another virus.
The World Health Organisation (WHO) has not yet confirmed the Pakistan outbreak but has requested more information from the government.
One boy in Thailand and six people in Vietnam have died from the recent H-5N1 bird flu outbreak
There is no evidence that the flu can be transmitted from humans to humans, but the WHO warns the Asian outbreak could mutate and become more dangerous.
Pakistan is now the eighth Asian country to have registered current cases of bird flu.