The privately-owned Esther Miracle went down in calm waters last Thursday carrying 161 passengers and crew from the capital Libreville to the oil town of Port-Gentil.
Most of the 124 survivors were picked up off Libreville after dawn on Thursday by locals in dugout canoes, fishermen, an oil barge and a navy patrol boat.
"A ship with divers is trying to locate the wreck," said Prime Minister Alain-Claude Bilie-By-Nze on Sunday, when the three bodies were found.
"We will not stop the search until we locate the wreck and are sure we have brought up all the bodies," he added.
Libreville public prosecutor Andre Patrick Roponat told AFP on Thursday an inquiry had been launched to see whether negligence, poor maintenance or "factors beyond human control" caused the accident.
Pending the outcome of the investigation, the Gabonese government suspended overnight passenger ship voyages until at least March 31 and ordered an audit of all passenger vessels.
Most of the 124 survivors were picked up off Libreville after dawn on Thursday by locals in dugout canoes, fishermen, an oil barge and a navy patrol boat.
