Mr Sonowal also said that a mechanism has to be devised "humanely" by the central government on what to do with those who are found to be illegal immigrants after finalisation of the National Register of Citizens (NRC), a list of the state's citizens.
"There is no question of discriminating against anyone whether he or she is a Hindu, Muslim, Bengali or Nepali," Mr Sonowal told PTI.
No one will be victimised on the basis of caste and community, he asserted.
"All will be treated equally and given opportunities to prove their citizenship so that their names could be incorporated in the subsequent drafts of the NRC," Mr Sonowal said.
The chief minister said the NRC has given an opportunity to segregate the bona fide citizens from illegal immigrants and it is a "win-win situation" for those who have been living under the stigma of "suspected illegal immigrants" for the last four decades.
"The government is working reasonably as per the Supreme Court order. Those who will be found to be illegal immigrants after the final list will also be treated humanely. A mechanism has to be evolved by the central government on what to do with them," he said.
The part draft of the NRC was published on the intervening night of December 31 and January 1 where names of 1.9 crore people out of the 3.29 crore applicants were incorporated.
The massive exercise aimed at identifying illegal immigrants in the state that borders Bangladesh is being carried out in Assam following a decision in 2005 after a series of meetings between the central and state governments and the influential All Assam Students' Union (AASU).
Assam, which faced influx of people from Bangladesh since the early 20th century, is the only state having an NRC, first prepared in 1951.
The current exercise, started in 2005 under the then Congress regime, got a major push only after the BJP came to power in the state with illegal immigration from Bangladesh as a poll plank.
The Supreme Court, which is monitoring the entire process, had ordered that the first draft of the NRC be published by December 31 after completing the scrutiny of over two crore claims along with that of around 38 lakh people whose documents were suspect.
Of the 3.29 crore applications submitted, there was confusion over the inclusion of 29 lakh people who had submitted certificates issued by 'gram panchayats' as proof of identity, after a Gauhati High Court order in February had deemed 'panchayat' certificates invalid, an official said.
The Supreme Court set aside the High Court order and upheld the validity of the certificates as identity proof if they were followed up with proper verification.
The top court also asked authorities to stick to the original deadline for the publication of the draft NRC and include names of those whose claims were verified.
When the NRC was first prepared in Assam way back in 1951, the state had 80 lakh citizens then.
The process of identification of illegal immigrants in Assam has been debated and become a contentious issue in the state's politics.
A six-year agitation demanding identification and deportation of illegal immigrants was launched by the AASU in 1979. It culminated with the signing of the Assam Accord on August 15, 1985, in the presence of then prime minister Rajiv Gandhi.