The Centre had asked all states to take biometric details of Rohingyas and other illegal immigrants living in their jurisdiction as part of a countrywide security exercise, home ministry officials said on Friday.
The move has been taken so that illegal immigrants can be identified as they move to different parts of the country.
The state governments have been told to instruct the local police to capture the biometric details of Rohingyas and other illegal immigrants, according to a senior home ministry official.
Around 14,000 Rohingyas living in the country are registered with the United Nations High Commissioner for Refugees, while about 40,000 are said to be staying illegally.
Home Minister Rajnath Singh had said in Parliament in July that some Rohingya Muslim migrants in India have been found indulging in illegal activities and maintained that security forces have been deployed to stop their infiltration into the country.
The official said capturing the biometrics details does not mean that they will be given any valid identification document.
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Documents such as Aadhaar can be issued only to those non-citizens, who visit India legally and are residents in India for minimum six months but the Rohingyas, being illegal migrants, do not qualify for it, the official said.
The Supreme Court Wednesday had also directed the government not to issue Aadhaar card to illegal immigrants.
Calling all Rohingya in India "illegal immigrants", the home minister had said Thursday the state governments have been asked to observe their movements and obtain their personal details so they could be deported to Myanmar.