The Goa government had demanded that the letter 'exempting' Karnataka from obtaining Environment Clearance (EC) for a project on the river either be kept in abeyance or withdrawn.
Fernandes was a leader of anti-merger movement supporting the cause of Goa remaining as an independent state during the historic 1967 Opinion Poll.
He submitted his resignation in response to the demand made by Goa Sports Minister Manohar Ajgaonkar.
Days after 10 Congress MLAs in Goa joined the BJP, CM Sawant reshuffled his cabinet, dropping three members of ally GFP and an Independent legislator as ministers.
Naik was the President of Goa Pradesh Congress Committee who had resigned from the post recently after party chief Rahul Gandhi appealed for the young minds to take over the reigns.
The Congress Goa in-charge has claimed that if given a chance they can prove their majority in the assembly within seven days.
The First Information Report was filed against the senior Congress leader for allegedly amassing disproportionate assets worth Rs 4 crore.