Legislators Nemcha Kipgen and Vungzagin Valte submitted their resignation letters to party president TN Haokip as well as to speaker Th Lokeshwor, they said.
With the resignation, the strength of Congress has gone down to 45 seats in the 60-member Manipur assembly. Kipgen had been elected in the last assembly polls from Kangpokpi constituency which had recently been upgraded into Kangpokpi district.
Valte was elected from Thanlon assembly constituency. Vice-president of Manipur Pradesh Congress Committee S Achouba also resigned from the primary membership of the party.
Incidentally, the state's move to carve out seven new districts has triggered protests by Manipur's apex Naga organisation United Naga Council. Last year, three veteran Congress heavyweights N Biren, Y Erabot and Francis Ngajokpa had resigned and joined the BJP.
Elections for the 60-member Manipur assembly will be held in two phases, on March 4 and March 8.
BJP, which is in direct fight with the Congress in the state, is unlikely to project any chief ministerial candidate.