The apex court ordered the Centre and the states to take measures so that the cow vigilantes do not take the law into their hands.
The top court has also asked the petitioners to file a petition questioning the large scale animal slaughters which occurred during Eid.
"You (petitioners) know how large number of animals were slaughtered just a few days ago. You must also file petitions against it," the SC told the petitioners.
Indira Jaising and Colin Gonsalves, two of the petitioners, said the number of incidents of cow vigilantism kept on increasing though the central government reacted against such activities, The Times Of India reported.
The apex court also said the Centre cannot wash off their hands calling it a state issue as per the Constitution.
The bench has asked chief secretaries of each state in consultation with the DGP to take measures to keep the highways safe.
In last few years, several cow vigilantisms has occurred in the country.
One of the recent attacks which shook the nation was the stabbing of a 16 years old Junaid Khan on a Haryana bound train, who was accused of carrying beef and later attacked.
The deceased, who hails from Ballabgarh, Haryana, has been identified as Junaid, 16, who was travelling home with his brothers Haseem, Moeen and Mohsin after shopping for the upcoming Eid at Delhi's Jama Masjid.
PM Modi raised his voice against these activities during a visit to his home state Gujarat months ago. "Killing people in the name of Gau Bhakti is not acceptable. This is not something Mahatma Gandhi would approve."
"We come from the land of non-violence," the PM said, "Violence won't solve any problem" he added.
However, hours after Prime Minister's condemnation on cow vigilantism, a man was killed in the state of Jharkhand for carrying beef in a car on June 29.
Alimuddin, also known as Asgar Ansari, was driving his Maruti car while he was stopped by a mob in Ramgarh district and beaten up. Though Alimuddin was taken to a hospital by the police, he soon died.
Apart from this incident, a dairy owner was attacked three days before Jharkhand attack by a mob after they saw the carcass of a cow. The mob resorted to set his house into fire.
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