It has effectively left the Congress strength to 20, equal to that of the ruling National People's Party (NPP), which is running a coalition government in the north-eastern state with the BJP and some regional parties.
The election for the 60-member Meghalaya assembly was held in February last.
Mr Danggo submitted his resignation to Deputy Speaker Timothy D Shira in the absence of Speaker Donkupar Roy late last night.
"I hereby tender my resignation of my seat in the assembly from Ranikor (ST) assembly constituency with effect from June 21, 2018," he said in his resignation letter.
He also intimated state Congress president of his decision to resign as the lawmaker as well from the primary membership of the party.
"As per the desire of my people, I have tendered my resignation as lawmaker with effect from June 21, 2018," Mr Danggo said in his letter to PCC president.
"Therefore, with deep sorrow and regret in my heart, I am also resigning from the primary membership of Congress along with all positions that I am holding in the party with effect from June 21," he said.
Mr Danggo, the five-time Congress lawmaker from Ranikor in South West Khasi Hills district, is likely to join the ruling National People's Party (NPP), sources close to him said.
Home Minister James K Sangma confirmed the resignation of Mr Danggo, saying it has been accordingly accepted.
After announcing on June 12 that he would quit, Mr Danggo had put on hold his resignation following the cancellation of a cabinet meeting that was supposed to clear a proposal to set up a subdivision at Ranikor. The meeting was postponed as the chief minister was not keeping well.
Mr Danggo submitted his resignation late last night.
With the latest development, the Congress strength in the House has been reduced to 20, same as the ruling NPP.
The ruling Meghalaya Democratic Alliance (MDA) comprises 20 lawmakers of NPP, 7 of United Democratic Party (UDP), four of newly-formed Peoples Democratic Front (PDF), and two each of BJP and Hill State Peoples Democratic Party (HSPDP).
The NCP, with one lawmaker, and two independents are also supporting the government.