The deadly incident took place in Alwar district in the desert state of Rajasthan.
Alwar’s police chief Rahul Prakash confirmed on Wednesday that Pehlu Khan, 55, had died in hospital two days after a group attacked his cattle truck on a road in the region.
“We are yet to receive the postmortem report, but [the victim] had multiple rib fractures,” the official said.
Prakash added that at least six others were injured in the assault.
Police have listed more than 200 people as suspects in the murder case and posted a reward to help identify the attackers.
The Muslim was driving in a convoy of six cattle transport trucks when the mob intercepted his vehicle. A video of the attack was broadcast on Indian television, showing the man being beaten with sticks and iron rods.
Rajasthan's Home minister Gulab Chand Kataria said on Wednesday the vigilantes had “done a good job by protecting cows from smuggling”.
“But they have violated the law by beating people brutally,” the minister added.
This is the latest assault in a spate of mob killings in the name of the revered animal in India.
In September 2015, a Muslim man from a village near Delhi was lynched after being accused of storing beef in his freezer.
In August last year, videos emerged showing young Dalits, India’s least socially dominant caste tasked with disposing of dead cows, being flogged for handling the animals’ carcasses.
Another five people were injured in clashes in the capital, Delhi, this week after a woman was accused of warding off a cow by throwing stones at the animal.
Gangs of “cow protectors” have been implicated in killing at least 10 people in the past two years.
Police are regularly accused of working alongside cow-protection vigilantes.
The developments come as demands by right-wing Hindu groups to stop the slaughter of cows, considered holy in Hinduism, could fuel communal tensions with Muslims.
India’s Prime Minister Narendra Modi won office in 2014 pledging to ban beef across India.
Slaughtering cows is banned in many states of India, where the majority of the population is Hindu. The move has been seen by religious minorities as a sign of the growing power of hard-line Hindus.
Beef consumption is now permitted in only eight of the country’s 29 states and territories.
Last week, Modi's home state of Gujarat raised the sentence for cow slaughter to life imprisonment. The chief minister of another state, Chhattisgarh, said at the weekend that anyone caught killing cows there would be hanged.
India’s ruling Hindu nationalist Bharatiya Janata Party (BJP) recently ordered the closure of abattoirs operating without licenses across several states, a move seen as alienating the country's Muslim population.
Several incidents of violence against Muslims and other minority groups have fueled concerns as religious intolerance is growing under the Hindu nationalist government.
India's history is pockmarked by horrific Hindu-Muslim communal clashes in the past.
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