The banca, some seven meters long, had nine passengers when it capsized off Isla Taber at about 2:30 pm. on Thursday.
Seven of the passengers were immediately rescued by a composite team of the local police, the Philippine Air Force (PAF) and the provincial disaster council.
In an interview, Inspector Rolando Bartolome, Lake Sebu police chief, told The STAR that the bodies of Mayjoy Lazo, 11, and Rosalyn Ankoy, 14, were found separately by the rescue team after four days of scouring the vast lake.
He said Lazos body was found floating 200 meters away from Isla Grande at around 6:30 p.m. while Ankoys body was found floating 500 meters from Lazos body.
Bartolome said Lazos and Ankoys remains were brought to the town proper and was placed under "post mortem examination" under Dr. Jocelyn Bayquin, the municipal health officer of Lake Sebu.
Lake Sebu Mayor Basilo Salif thanked all the concerned government agencies, especially the provincial PNP command, PAF and the disaster councils, which participated in the search and rescue operations.