Unofficial estimates say there are around 35,000 madrasas with around 15 lakh students.
The Centre is likely to conduct a survey in states along the international border to check whether foreign nationals are employed in madrasas.
The move comes after reports that Bangladesh nationals were teaching students at a madrasa in Burdwan, where a blast on October 2 indicated the growing presence of Bangladeshi terrorists.
National Security Advisor Ajit Doval, has already visited Bengal and expressed displeasure about the state government's less than sharp eye on the security aspect.(Read:
PM Modi's Top Adviser Visits Burdwan Blast Site, Meets Mamata Banerjee)
West Bengal and Assam other two key states which share borders with Bangladesh.
A recent internal report of the home ministry, however, said a majority of the madrasas are not spreading jehadi activity in India. The report was based on madrasas run by four different Islamic schools - Deoband, Al Hadis, Jamiat and Barelvi.
It has only red-flagged madrasas which have teachers of Bangladeshi or Pakistani origin, saying there are examples of such madrasas actively radicalising young minds.
On November 6, Moulana Mahmood Asad Madani of the Jamiat Ulema-e Hind had objected to the haste with which madarasas were being branded terror hubs. He also said the madrasas recognized by the government were not doing the real job. It was being done by the unrecognized ones. (
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There is no official figure about the number of madrasas in the country. Unofficial estimates put the figure around 35,000, with around 15 lakh students. Most of these are unrecognised by the government.
The survey is likely to start with the states along the international border - West Bengal, Assam, Uttar Pradesh and Bihar - and gradually may be extended.