The NRC State Coordinator cited a few examples of anomalies committed during the updating of the register.
According to unverified reports, the affidavit contained the names of around 4,800 persons.
Some of the petitions in the apex court have also raised the issue regarding the process of delimitation in Nagaland and Manipur.
Leader of Opposition in the Assembly Debabrata Saikia said the NRC authorities in Assam had not obtained SC nod to issue the directive.
The statement comes amidst criticism of the government for its failure to begin an exercise where the over 19 lakh people left out of the final NRC can challenge their exclusion.
The TMC lawmaker had asked the Home Ministry about detention centres in Assam and their capacity.
The Rejection Slip will mention the reasons for excluding a person's name from the final NRC.
Sarma also said the matter was of utmost importance as the details have to be submitted to the Registrar General of India urgently.
Through the 'memo' issued on February 19, NRC state coordinator Hitesh Dev Sarma had asked all the DMs to submit the details by February 20.
It named four alleged 'jihadis' stating that they became genuine Indian citizens by virtue of the NRC.
NRC state coordinator Hitesh Dev Sarma did not answer queries made through WhatsApp
'As an IT services provider, Wipro was tasked with providing the technical architecture and technology solutions for the project,' it said.
The data was not available for the last couple of days and it created panic in the public, mostly among the people excluded from the list as the rejection certificates were yet to be issued.
Government said the approved standard operating procedures for disposal of claims and objections had specific provision for children who got left out from the draft NRC.
He also said that the National Register of Citizens (NRC) would be updated again.