Hundreds of people took part in a protest on Friday to decry perceived negligence on the part of the authorities in connection with Tuesday's boat mishap on the Congo River, some 50km west of Kisangani.
Protesters looted the office of the General Directorate for Migration, along with another government office, before setting both buildings ablaze.
The ensuing fire gutted both structures, including administrative files.
Demonstrators also prevented fishing boats from using the river.
Congolese authorities have not yet announced the number of people killed in the boat mishap.
Some civil society organizations, however, have said that around 41 people were killed, while another 60 were missing.
One demonstrator blamed the authorities for the tragedy.
"The government does not properly monitor the transport and fishing sectors," he told The Anadolu Agency, preferring to remain anonymous.
The protest was led by a group of young people who have been lobbying for the reform of the river transport sector. They accuse the authorities of turning a blind eye to violations by ferry owners, such as loading river ferries beyond capacity.
The authorities have opened investigations into the mishap, vowing to punish those found responsible.
They have yet, however, to comment on the demonstrators' allegations of negligence.