He and other celebrity chefs argue that conditions in such farms are unacceptable and that supermarkets are partly to blame for this for selling chickens too cheaply.
He had urged shareholders to support his motion, which would have required Tesco to adopt higher minimum standards for chickens it purchases.
Had the proposal been backed by shareholders, Tesco would have had to adopt the RSPCA's freedom farm standards on how birds are fed, exercised and transported.
Farms approved by the RSPCA for meeting "higher welfare" standards are able to carry the freedom farm logo on their products.
Tesco says it has adopted such standards on a growing number of its farms, but that to do so universally straight away would force up the price of chickens and that this would be unpopular with families already facing higher shopping bills.
Mr Fearnley-Whittingstall said he was "disappointed" that Tesco had chosen to "abdicate responsibility" on the issue of poultry welfare to the government and shoppers.
But he said he was encouraged that "significant changes" were taking place "behind the scenes" in Tesco's policies and called on the UK's largest supermarket chain to take the lead in establishing a forum to discuss general poultry welfare issues.
"The way chicken has been sold in this country has been a bit of a secret for some time," he said.
"I would like to see some real change from Tesco in the coming months."
Tesco, which accounts for more than a fifth of all intensively reared chickens sold, was criticised earlier this year when it cut the retail price of its standard whole chicken to £1.99.
Tesco said its welfare standards were "amongst the best in the world" and that the share of higher welfare chicken it sold had risen 70% in the past year.
"We have been working hard for a while to increase the amount of higher welfare chicken we sell and the recent debate over chickens in the media has helped raise awareness of the choice available to customers," a spokesman said.
Shareholders pressed Tesco bosses on a range of issues
But it added: "A large number of our customers are on a tight budget and rely on lower cost foods to feed their families. We believe it would be wrong to remove these options for them."
Corporate governance firm PIRC, which backed Mr Fearnley-Whittingstall's resolution, said it had not expected to win the vote but that it had raised awareness of the issue.
Higher standards would create a "more enriched environment" for chickens and would ultimately be healthier for customers, it added.
Other issues debated at the meeting ranged from calls for union recognition at its new US stores to allegations of low pay for workers employed by global suppliers, particularly in India.
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