By Wednesday, of the 3,175 samples collected from live poultry markets and farms, 34 samples in Shanghai, Anhui, Jiangsu, and Zhejiang provinces contained the H7N9 virus, according to the Ministry of Agriculture.
But Hou said the industry is suffering undeserved losses since the H7N9 virus will not easily spread among poultry.
Also, the relationship between the virus detected in poultry and the virus that has infected humans has yet to be determined, he said, citing a statement from the ministry on Monday.
China produced 18.23 million tons of poultry meat and 28.61 million tons of poultry eggs in 2012, according to the National Bureau of Statistics.
"It is a certainty that the industry will shrink this year. Now I am also quite worried that many farmers may give up poultry farming in the future, since there are so many risks in the sector," Zhao said.
As of Friday, 43 people had contracted the H7N9 virus in China, 11 of whom had died.
More than half of the confirmed H7N9 bird flu cases in Shanghai had been in contact with live poultry recently, though the source of this lesser-known virus is still unknown.
Some of them worked in the business of live poultry while some bought live poultry at local markets, Shanghai's medical experts said.
"Our research on the city's cases showed that more than half of these infection cases were related to live poultry. One of the effective ways of preventing infection is to avoid contact with live poultry," said Zhang Wenhong, director of the infectious diseases department of Huashan Hospital in Shanghai, at a lecture on H7N9 prevention and control on Thursday.
So far, the city has shut down 23 unlicensed poultry trading stalls and 119 roadside live poultry stands, and 34 flower and bird markets have been ordered to stop trading.
Most of the city's H7N9 cases have been found among elderly people, partly due to their weaker physical health and immune system, according to doctors.
Special report: H7N9 avian influenza
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