Seven-year-old Stacy Lemmens and Nathalie Mahy, 10, went missing on the night of June 9 while playing at a street fair in Liege.
Cedric Visart de Bocarme, the Liege chief prosecutor, said on Wednesday that "this morning, around 11am (0900 GMT), Stacy was found dead and this afternoon it was Nathalie whose corpse was discovered, during a new search launched in parts of Liege."
The bodies were found about 10 metres apart in a storm drain among dense undergrowth beside a railroad track less than 500 metres from the cafe where the stepsisters were last seen before they disappeared.
"The hunt for the culprit or culprits is now a priority and everything possible will be done to shed light on the case as soon as possible," said Visart de Bocarme.
Only an autopsy will be conducted to establish exactly how the children were killed, although another Liege prosecutor, Anne Bourguinont, said: "This can't be considered to be an accident."
Only one suspect in the case has been publicly named but police have acknowledged that they found no evidence linking the man, Abdallah Ait Oud, 38, to the girls' disappearance.
He has denied being involved but has said he was in the area around the time they went missing.
The bodies were found in a storm
drain beside a railway track
Their case has revived disturbing memories of the Marc Dutroux paedophile crimes in the 1990s.
The killings have revived dark memories of the Marc Dutroux paedophile crimes in the 1990s.
Dutroux kidnapped and raped six girls, one as young as eight, and murdered two of them.
Two others starved to death in a makeshift dungeon after he was sent to prison for a minor offence.