[14] From November 2006 to January 2007, when an acute national political impasses arose in Bangladesh out of uncertainty about Parliamentary elections, he performed the role of the President's special envoy in the negotiation process.

He tried to reconcile issues between the two opposition leaders, Begum Khaleda Zia of the Bangladesh Nationalist Party, and Sheikh Hasina of the Awami League.

Chowdhury used good offices of the western diplomats led by the US Ambassador Patricia A. Butenis and stopped the martial law while the army group had to retreat to the option of the state of emergency, which was supported by all political parties for their own interests.

Responding Chowdhury's all these initiatives Special Envoy Craig Jennes led a two-member UN delegation to Bangladesh and finally Patricia A. Butenis and Anwar Choudhury met Principal Staff Officer General Jahangir Alam Chowdhury and Chief of Army Staff General Moeen U Ahmed, transmitted message not go ahead with their martial law option and informed if it happens Bangladeshi Peacekeepers will be back from the UN Peacekeeping Mission and there will be sanctions imposed on Bangladesh by the UN.

In that event, negotiations had been led by the then-Commonwealth Secretary General Chief Emeka Anyaoku's special envoy Sir Ninian Stephen.

[23] Chowdhury later said that General Moeen, Army Chief, was the main force in the military intervention[24][25] and declaration by President Iajuddin Ahmed of a state of emergency on 11 January 2007.

According to Amar Desh reporting in 2009, Chowdhury said that Moeen had intended to capture the country's presidency through the interim Caretaker Government headed by Fakhruddin Ahmed, formerly with the World Bank.

[36][37][38] Chowdhury later said that General Moeen, Army Chief, was the main force in the military intervention and declaration by President Iajuddin Ahmed of a state of emergency on 11 January 2007.

According to Amar Desh reporting in 2009, Chowdhury said that Moeen had intended to capture the country's presidency through the interim Caretaker Government headed by Fakhruddin Ahmed, formerly with the World Bank.

[39] Chowdhury brought all the political parties including agitating Grand Alliance in the parliamentary election of 22 January 2007 after having a series of meetings with them and agreeing to their demands.

Chowdhury was fighting against Moeen and Aminul Karim's group as they were making army deployment of Caretaker Government (CTG) dysfunctional in November 2006, managing four advisors' resignations in December 2006 what he was also able to replace and stopping martial law and the State of Emergency until 11 January 2007.