The top court said the certificates issued by the Gram Panchayat secretary merely acknowledges shifting of residence of a married woman from one village to another.
"The certificate by itself and by no means establishes any claim of citizenship of the holder of the certificate," a bench of Justices Ranjan Gogoi and R F Nariman said.
It said "such proof will come only if the link between the claimant and the legacy person (who has to be a citizen) is established".
Various individuals and organisations had challenged the high court order which had held such certificates as invalid for making claims for inclusion in the National Register of Citizens (NRC).
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The bench made it clear that the certificates issued by the Gram Panchayat Secretary or Executive Magistrate will be acted upon only to establish a linkage between the holder of such certificate and the persons from whom legacy is being claimed.
The court said such certificate was a supporting document for making a claim of citizenship and only enabled its holder to establish a link between him and the person from whom legacy is claimed.
The bench noted that in several reports of the state coordinator of NRC Assam, it was made clear that a claim made by such a certificate, without details of the legacy person, is to be discarded.
The apex court said the certificate has to be verified at two stages-- first is the authenticity of the certificate itself and the second, the authenticity of its contents.
It said the second process of verification was bound to be an exhaustive process as the source of information and other details recorded in the certificate have to be ascertained while also giving an opportunity to the holder of the certificate.
It said that view of high court and submission of Assam government that such certificates are "private document" cannot be sustained as Assam Panchayat Act gives jurisdiction for issuance of such documents by the concerned authorities.
About 48 lakh claims have been made using certificates issued by Gram Panchayat secretaries, out of a total of 3.29 crore claims made so far for inclusion in the NRC which is being prepared in Assam to identify illegal migrants.
NRC coordinator Prateek Hajela had earlier informed the court that out of the 48 lakh claims made for NRC, 20 lakh were the indigenous people of the state and if the fact of being original inhabitants of the state is established, then no further verification is required.
In a separate verdict, the apex court refused to give clarification to the meaning of the term "originally inhabitants of the State of Assam" saying the exercise of NRC upgradation was not intended to be one of identification and determination of who the original inhabitants are.
"Citizens who are originally inhabitants/residents of the State of Assam and those who are not, are at par for inclusion in the NRC," it said.