"In the garb of the order that prohibits the trading of cattle at organised markets, the government has tried to impose a ban on the meat industry," Abdul Faheem Qureshi, head of the Muslim All India Jamiatul Quresh Action Committee, told Reuters.
"Meat supplies will very soon grind to a halt in India and abroad if either the government does not repeal this draconian order or a court does not step in," Qureshi said.
Government officials were not avaibale for comment.
Indian meat traders, under the aegis of the Quresh Action Committee and other trade and industry associations, plan to petition India's Supreme Court in the next couple of days to get the government order rescinded.
"Exports will come to a halt because slaughterhouses will find it extremely difficult to buy cattle and we also apprehend widespread job losses in the sector, which supports millions of people," said Qureshi.
Abattoirs across India on March 31 called off a strike after four days when the most populous state of Uttar Pradesh, ruled by Modi's party, gave assurances that it would renew the licences of slaughterhouses and protect them against the attacks from cow vigilante groups.
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The slaughter industry stabilised after the strike but the latest order has unsettled trade again, said Priya Sud, partner at Al Noor Exports, which operates abbatoirs in Uttar Pradesh.
The impact on exports will be more evident after a couple of months when the supply chain dries up, Sud said.
India exported 1.33 million tonnes of buffalo meat in the 2016/17 fiscal year to March 31, worth about $3.9 billion. The exports were slightly up from the 1.31 million tonnes exported in the previous year.