Pitted against BJP's state chief Vinay Tendulkar, Naik expressed confidence of winning the election with the "support of like-minded secular forces."
The Congress yesterday announced that Naik will be party's candidate for the election to the state's lone Rajya Sabha seat to be held on July 21.
Naik, who was accompanied by Leader of Opposition in the state Assembly Chandrakant Kavlekar and other Congress legislators, submitted his form to state Legislature Secretary N B Subhedar.
"I am fully confident that I will be the winner. We will approach all the secular-minded people who are supporting the BJP-led alliance," Naik said hinting at a possible dialogue with the BJP's allies - Goa Forward Party, Maharashtrawadi Gomantak Party and independents - for the support.
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Naik, who was recently appointed as the president of Goa Pradesh Congress Committee, said he was thankful to the party high command for choosing him as the candidate for the Rajya Sabha poll.
Earlier in the day, the BJP state unit president, Vinay Tendulkar, filed his nomination for the election.
Tendulkar has the support of 12 legislators from his own party, three each from allies Goa Forward party and the Maharashtrawadi Gomantak Party and three independents.
Naik is expected to get the support of 16 MLAs of his party and the lone Nationalist Congress Party legislator.
The 40-member Goa Assembly currently has a strength of 38 with one MLA each from the Congress and the BJP having resigned after the state polls held earlier this year.