Ngajokpa is the third Congress MLA to quit the party in the past one month before the 2017 Assembly polls in the state.
The resignation has not affected Congress' strength in the house as four MLAs of Trinamool Congress had joined it recently.
Congress now has 49 members in the assembly, which now has an effective strength of 53 instead of 60 after three Congress MLAs and four of Naga Peoples Front resigned from the House recently.
The decision though was taken following demands of the electorate of Tadubi constituency which he represents, he said.
Ngajokpa has sent his resignation to Speaker Thokchom Lokeshwar Singh, Assembly secretariat sources said.
The move today follows intense pressure from his workers who urged him to resign from Congress during the MLA Workers Meeting held last week in Senapati district.
Manipur PCC President T N Haokip told media there was no restriction for an MLA to leave the party and the decision of all individuals are always respected by it.
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