Customs officers at Dhaka airport, acting on a tip, opened the luggage of two Indian national who were flying to Bangkok and found the tortoises estimated to have a value of $35,000 on the black market.
It is thought the animals were collected in India and Dhaka was being used as a transit point.
Conservationists say smugglers are increasingly using Bangladesh as a route for the illegal transportation of wild animals such as the confiscated tortoises, which are popular as exotic pets and for their meat, believed in Asian medicine to have medicinal value.
More resources are needed to tackle the problem, they said.
Conservationist Anisuzzaman Khan told the BBC not enough checks were being made at airports and sea ports in Bangladesh.
Last year officials in Thailand discovered hundreds of tortoises, turtles and crocodiles in a suitcase arriving on a flight from Bangladesh.