The ship carrying the Bangladeshis will bring back Myanmar security personnel who crossed the border recently amid fighting with rebels
A special SriLankan Airlines jet left Shahjalal International Airport with the Australians on board Saturday morning.
High Commissioner Jeremy Bruer was at the airport to see them off.
Earlier, 285 Australians returned home from Bangladesh in the first flight.
Australia has brought back about 15,000 of its nationals from different countries amid the coronavirus outbreak.