A cargo flight carrying the shipment, the third from Japan, took off from Narita International Airport around 9pm on Monday, the Bangladesh embassy in Tokyo said.
The vaccines will arrive in the country via Hong Kong on Tuesday, the embassy said.
The government on Monday began administering the second doses of AstraZeneca shots arriving from the island nation under the global COVID-19 vaccine-sharing initiative COVAX.
Along with the latest shipping, the number of doses arriving from Japan totalled to 1.6 million. As many as 1.5 people lined up for their second jabs in Bangladesh on Sunday.
Bangladesh started its mass vaccination campaign in February, using the vaccine developed by the University of Oxford and Anglo-Swedish company AstraZeneca, bought under an agreement with the Serum Institute of India.
Apart from that, India also gifted 3.2 million doses of the shot to Bangladesh in two phases.
The inoculation drive resumed after the government received consignments of Sinopharm vaccine from China, and Pfizer-BioNTech and Moderna vaccines under COVAX.
The second phase of the mass inoculation programme with the Sinopharm doses began at 67 centres across the country on Saturday. China sent 1.1 million shots as gift on May 12 and Jun 13.
However, the timeline for those who took their first shots with AstraZeneca was disrupted as no other vaccine could be administered on them.
Earlier, Japan shipped a total of 1.02 million doses in two separate consignments as part of its promise to gift Bangladesh with a total of 3 million shots under the COVAX platform.