Jesuits in Social Action (JESA) is calling for "urgent measures" to stop hate crimes against Christians and other groups.
It claims there has been a rise in hate speeches against Christians since Narendra Modi took office in May.
JESA told Catholic news agency Fides: "Their identity is mocked, their citizenship questioned, their faith ridiculed. Coercion, divisions and suspicions multiply. Attacks against religious minorities have assumed alarming proportions."
"Daily low-intensity violence... is becoming routine."
"The hatred, violence campaign and threats have left not only religious minorities speechless, but also civil society, lawyers and academics, while the government remains silent.
"The Christian community has been the target of mob violence in Uttar Pradesh, Madhya Pradesh and Chhattisgarh."
JESA also claims many perpetrators of religious violence are not punished by the authorities.
Prime Minister Modi has been criticised by some for not doing enough to stop riots that occurred in 2002 in his political province of Gujarat. However, he denies the accusations.
More than 1,000 people died in the violence, most of whom were Muslim.
Just over 5% of India's population is Christian.