Since coming to power in May 2014, Modi and his National Democratic Alliance (NDA) have come in for criticism for their lack of work to tackle persecution.
A number of high profile attacks have been reported on Christians in the past 24 months including the rape of an elderly nun at a school.
The Catholic Secular Forum says there has been a 20% rise in persecution in 2015 with 365 major attacks.
International Christian Concern has documented 102 separate attacks on Christians and their places of worship since the beginning of 2016.
These attacks range from the vandalism of churches, to the beating of church leaders and parishioners, the charity said.
"It is the hate speech and incitement to violence by ranking members of government and the RSS that continues to mark Modi's second year of his five year term," Dr John Dayal, Spokesman of the United Christian Forum, told ICC. "This violence, sharp and shocking as it is, seems to fade into the background [in India]."
"Almost on a daily basis we are facing difficulties," a pastor of an independent church in India told ICC. "New problems and accusations are being levelled against Christians by Hindu fundamentalists. [Christians] fear these challenges are the Ache din (good days) our prime minister promised at his election. Looking to the future, it appears that the worst is still ahead of us."
ICC's Regional Manager for South Asia, William Stark, said: "Another difficult year has passed for Christians in India.
"Prime Minister Modi and his government have done little to protect the religious freedom rights of religious minorities in India, including Christians.
"Hate speeches against religious minorities have gone unchecked. Attacks on Christians and their places of worship have gone unpunished. Outright cases of persecution and discrimination have gone unopposed.
"This lack of action has created an atmosphere of impunity for radical Hindu nationalists seeking to violently turn India into a nation exclusively for Hindus. It is time for India and its leaders to take action and reverse this trend.
"India cannot continue to ignore the deterioration of religious freedom within its borders. The government must take steps to protect the religious freedom rights of all its citizens, including minorities, and punish those who violate those rights.
"If this is not done, religious freedom in India will continue to deteriorate and 2016 may overtake 2015 as the worst year for religious freedom in India's independent history."