President Abdul Hamid and Prime Minister Sheikh Hasina - Sheikh Mujib's daughter - paid their tributes and offered wreaths on the portrait of 'Bangabandhu' at his Dhanmandi residence followed by a state salute by an army contingent.
Hamid and Hasina later visited Sheikh Mujibur's shrine at southwestern Tungipara village.
Hundreds of people followed the Bangladeshi leaders in paying tribute, and recalling the horror when 32 people were killed as a group of rogue soldiers staged a coup in 1975. It was one the bloodiest political assassinations in the world.
Sheikh Mujib - fondly called 'Bangabandhu' (friend of Bengal) - was killed in the predawn raid at his Dhanmandi house along with his wife, three sons, two daughters in-law and several presidential aides and Awami League leaders.
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His two daughters - Sheikh Hasina, now prime minister, and Sheikh Rehana - escaped the bloodbath as they were in Germany.
"This brutality was a rare occurrence not only in the history of the Bangalee nation but also in the history of the world," President Hamid said in a statement.
Unrest followed the carnage, and then deputy army chief general Ziaur Rahman emerged as the strongman of Bangladesh. The regimes that took over protected the killers by enacting an indemnity law and rewarded several of the coup plotters with diplomatic posting abroad.
As the Awami league returning to power in a landmark election in 1996 after 21 years of political wilderness, Awami League scrapped the indemnity law and initiated a process of delayed trial of the perpetrators of the carnage.