In its findings, PETA (People for the Ethical Treatment of Animals), India, names companies including Venky's, Suguna Foods who allegedly indulge in such practices. The two companies have denied the charges.
PETA termed the practices "criminal" and urged the government to probe the issue.
Refuting the charges, Suguna Foods said it was not in the egg-business and therefore "there was no question of culling of male chicks".
"We are into the broiler-business where male and female chicks are reared together so it is a completely wrong allegation," a senior Suguna official told PTI.
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Nikunj Sharma, a PETA India official, screened a video in Hyderabad showing purported cruelty to animals allegedly at different hatcheries.
Poultry Federation of India President Ramesh Chander Khatri shared the companies' views saying while he could not comment on the videos, such practices were unheard of.
Addressing a press conference in New Delhi, PETA India CEO Poorva Joshipura said shortly after birth, male chicks are separated from female ones via a process known as 'sexing' which is extremely distressing as they hare handled roughly by workers.
"Hatcheries consider male (chicks) useless as only female (ones) can lay eggs. They are stored and killed in horrific ways," she said.
Male chicks- and others that are sick or considered unprofitable otherwise for meat or egg production- are killed in disturbing ways- "by grinding, drowning, burning, crushing and suffocation, or feeding them live to fish", she said.
Venky's DGM (sales and marketing) Omkar Verma questioned the authenticity of the videos shared by PETA and said male chicks are treated as byproducts for the companies in the layer sector, where egg laying poultries are raised.
Andhra Pradesh on the issue, Sharma said, adding the animal rights group would also be writing to the companies concerned soon, he said.
"In response to these atrocities, PETA is calling on the public to go vegan and the government to consider new 'in ovo' sexing technology, in which chicks' gender is determined before they hatch, potentially preventing large scale deaths of male chicks," Nikunj Sharma of PETA told reporters in Hyderabad.
The outfit also requested the government "to establish and implement a written standard for painless euthanasia for unhealthy chicks and take stern action against companies that kill chicks in cruel ways.