Police officers, firefighters and soldiers worked through the night in a desperate bid to find seven people still unaccounted for among the sludge and rubble.
Dozens of houses were buried when hillsides collapsed after torrential downpours in Hiroshima that saw more than a month's average rainfall descend in just three hours.
Throughout Wednesday there were moments of hope, with survivors who had sought refuge on the upper floors of their homes airlifted to safety, but there were also bodies carried away from the devastation wrapped in blankets or plastic sheeting.
It emerged Thursday that a 53-year-old rescuer who was killed in a secondary landslide the day earlier had died with a toddler in his arms.
Noriyoshi Masaoka, a firefighter with 35 years' experience, had battled through the slurry of the initial mountain collapse to rescue five people, before going back to help more.
The Tokyo Shimbun said a man and his three-year-old son were among a party of eight he was trying to rescue.
A witness told the paper the father had thrown his son into Masaoka's arms as he saw the second wave of mud and rocks beginning to cascade down the hillside.
But in a terrible twist of fate, the father reportedly survived the landslip unscathed and watched helplessly as it swallowed both the child and his would-be rescuer.
The bystander said the grief-stricken father remained where he was, just shouting his son's name.
- Vigil -
Members of a local high school baseball team were among teenagers who kept up an all-night vigil for one of their number, whose half-submerged house was the focus of floodlit efforts.
"I saw tweets (saying he was missing)," one youngster told Fuji Television.
"We went to the same junior high school. I want him to be found as soon as possible because he must be in pain," the boy said.
The network said the search at what remained of the property continued into Thursday but neither the boy, nor his father, had been found.
Aerial footage showed military personnel operating heavy machinery to clear debris and police officers pulling at trees that had smashed into houses.
Trained search dogs were also being taken over the muddy ground.
Among the 39 known victims were two brothers, aged two and 11, who were confirmed dead after being pulled out of their inundated home.
A neighbour who took part in the search told the Fuji network that the ground floor of the house was almost completely filled with mud.
"We collected shovels from the neighbourhood. The parents just had to believe the boys could hear them. They kept saying: 'Breathe!' and 'Reply!'
"The mother stood on the mud and just kept shouting," he said.
- Dire weather -
Rescuers were Thursday racing against the possibility of further bad weather, which threatened to dislodge more of the water-logged mountain.
Heavy rains have pummelled Japan in recent weeks, sparking landslides and floods in numerous parts of the mountainous and densely populated country.
In one of the districts hit by the tragedy, a record 217 millimetres (8.7 inches) of rain fell in the three hours to 4:00 am Wednesday, far more than the 143 millimetres that on average falls in August.
Landslides are not uncommon in Japan, despite widespread concreting to shore up hillsides, some of which are composed of fragmented granite that becomes unstable when saturated.
In October last year, dozens were killed when the torrential rains of a passing typhoon triggered mudslides on the island of Oshima, south of Tokyo.
In 1999, more than 30 people died in a series of landslides that hit Hiroshima, including the area affected on Wednesday.