The remains were exhumed "after water withdrew from two mass graves, which are several hundred metres away from each other," said Lejla Cengic, spokeswoman for the Institute for Missing People.
Flood water and landslides had revealed part of the graves near the Bosna river between the northern towns of Maglaj and Doboj, she told AFP, and the team then carried out further excavations.
The victims are believed to be Muslim men from the nearby village of Jablanica, who were killed by Bosnian Serbs in 1992, Cengic said. DNA analysis will be used in a bid to confirm their identities.
Bosnia's inter-ethnic war between 1992 and 1995 claimed some 100,000 lives. Thousands of missing persons have never been found.
The discovery of new mass graves has become relatively rare, though one was found in 2013 with the remains of more than 400 people.
Torrential rains hit Serbia, Bosnia and Croatia in mid-May, killing 77 people in the worst floods and landslides in more than a century.
The disaster forced the evacuation of tens of thousands of people and destroyed thousands of buildings and homes.
Bosnian authorities have also warned against the danger of landmines left over from the war which may have been dislodged by flood water and landslides.
More than 120,000 mines dating from the war still litter the country, with around 2.4 per cent of the country contaminated with the devices and other military ordnance.