The Catholic Secular Forum (CSF) said in a report to the Fides news agency that the radicals have infiltrated churches and Christian NGOs.
They are gathering information about church property and members of the Christian communities, including conversions and baptisms.
The CSF believes the information is being passed on to extremist political parties and terrorist organisations to be used against Christians.
Although Christians in most parts of India enjoy religious freedom, there are pockets in the country, most notably Orissa, where Christians are being targeted by radicals.
The CSF is concerned that the increasing tendency among Christians to post photos of their celebrations around the internet and on social networking sites is putting them at greater risk.
It fears that the information will be used by extremists to incite anti-Christian hatred and level false charges against them.
Recently, a pastor in Kashmir was arrested by police after a video surfaced on YouTube allegedly showing him baptising some Kashmiri Muslim men.
According to the Times of India, Pastor C M Khanna is accused of using money to persuade young boys and girls to convert.
The complaint against him also relates to photos on Facebook that are allegedly blasphemous against Islam.
According to Fides, the CSF warned that the information about Christians available on the internet may "generate a new wave of violence" against them.