One of the survivors, Shah Alam, filed the case with Gajaraia Police Station, said Harun-or-Rashid, officer-in-charge of the police station.
The accused are trawler driver Md Habib, 55, son of late Karim Bepari of Haji Shukur Hawladerkandi village in Shibchar of Madaripur, trawler owner Jakir Dewan, 45, son of Monnan Dewan of Akbarnagar village in Fatulla of Narayanganj and another unnamed.
Off them, Habib and Jakir are still absconding.
The trawler, carrying 34 workers from Cumilla, sank in the river at Charjhapta in Sadar upazila around 3 am on Tuesday after it collided with an oil-laden tanker while heading towards Fatulla in Narayanganj.
Although 14 workers managed to swim ashore, the rest went missing. All the workers hail from Pabna and Sirajganj districts.
Meanwhile, the search for the missing workers was being continued for the 3rd day on Saturday till filing of this report around 00:50 am.
Members of Bangladesh Inland Water Transport Authority (BIWTA), Fire Service, River Police and Bangladesh Coast Guard were trying to locate the trawler with the help of side-scan sonar system.