Laurent Vallier, 42, and his children have not been since September and the French embassy alerted the Cambodian authorities in November.
The embassy and police said it was impossible to establish the corpses’ identity on Sunday because of their badly decomposed state.
“We don’t know if it’s a question of robbery or murder,” said police official Touch Heang. “Let’s leave our team of experts work on it.”
But interior ministry official Chhay Sinarith said they were presumed to be Vallier and his four children, who were aged between two and 11 years old.
"Now we are appealing for witnesses who may recognise the clothes and the shoes we found in the car,” he said. “It's most likely the remains belong to the missing French family."
Chhay Sinarith said the bones of two children were found in a suitcase but a police officer late said the case was broken and the bones could have floated into it. The car is thought to have been in the pond for several weeks.
The parents of Vallier’s Cambodian wife, who died in childbirth in 2009, were among onlookers at the scene of the grisly discovery. They organised a ceremony of remembrance for the dead and seem convinced that the family was murdered.
“He would not commit suicide. I know his heart,” father-in-law Tith Chuon said.
Vallier, who according to his relatives worked as a tour guide, is thought to have moved from France to Cambodia about 12 years ago, arriving in Kampong Speu in 2007.