The top court told state governments and police chiefs to ensure there are no "attacks, threats or social boycott" over the February 14 bombing, the worst in the territory in three decades. Video footage of Kashmiris being taunted or beaten has been widely shared on social media, while right-wing Hindu groups and some TV news channel pundits have encouraged reprisals.
Some Kashmiris have been suspended by Indian universities for their social media comments on the case. Others have been arrested on sedition charges.
"Immediately after the attack, mobs and vigilante groups engaged in vitriolic hate speech and began attacking, and threatening Muslims and Kashmiris throughout the country," said two activists who sought the Supreme Court action.
Mohammad Yasin Khan, president of Kashmir Traders and Manufacturers Federation, told AFP that threats of violence were still being made. Khan said 300 students from Uttarakhand state alone have returned to occupied Kashmir.
Occupied Kashmir business groups called for a protest shutdown Friday by shops and stores in the territory against the "continuing threats and intimidation" of Kashmiri people in Indian cities.
'Pay a heavy price'
Analysts say military action is possible, and villagers in Pakistani Kashmir have been told to take precautions including building bunkers.