The bodies of the boy and a 26-year-old man were recovered on Sunday, two days after the police found four migrants who survived from a sunken boat on an island in the northwestern Bulgarian stretch of the Danube river, which borders Romania.
The migrants, who did not have any documents, told police they were a family of 10 people fleeing Iraq and that the metal boat which was carrying them to the Romanian coast on their journey to western Europe had capsized.
"We have been searching the river after the migrants told us that six people that were in the same boat with them have fallen into the Danube waters," Dimitar Chorbadzhiev, director of the regional border police said.
He said police officers are still searching for the three missing children, aged two, four and six as well as one man.
Bulgaria has built a fence on its border with Turkey in an attempt to stem migrant inflows and has asked Brussels to help it with police, specialized vehicles and tracking equipment to better protect its borders.