The figure makes the eruption of Mount Ontake, which was packed with hikers when it burst angrily to life on Saturday lunchtime, the worst volcanic disaster in Japan for almost 90 years.
Up until Sunday 36 bodies had been found, but many of these remained on the ruptured mountain as toxic gas and the risk of further eruptions forced emergency workers to suspend operations.
The grim news of more deaths came after media reports earlier suggested as many as 20 people remained unaccounted for, with an area of the volcano still spewing steam and gas.
An official at Nagano prefecture's crisis management office said helicopters had brought the dead from the mountain, whose pockmarked lunarscape bears witness to the huge volume of ash and rocks flung from the volcano.
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"We believe there are more people still missing, but we don't know how many they are," he added.
Broadcaster NHK said earlier in the day rescuers had seen more bodies that they had not yet been able to access.
But a local tourism association told the Asahi Shimbun that usually only 10 to 20 per cent of hikers register before entering the mountains in high season.
The report said 327 hikers had registered their presence on Mount Ontake at the time of the eruption.
Rescuers are hoping that many of those who cannot be contacted simply forgot to let mountain managers know they were safe.
Nagano prefecture has posted a notice on its website calling for information on hikers on the list.
"We don't know if there are people buried deep down under accumulated ash," a senior police official told the Asahi.
The local fire department said 71 people are missing, while the Nagano prefectural police have received hundreds of reports of people whose whereabouts are unknown, a police spokesman told AFP.
Authorities cautioned that some of these reports would likely have nothing to do with the disaster, which happened without warning during a busy weekend.
Hundreds of people were on the slopes of the volcano as rocks, ash and smoke poured from the fractured crater. Many made it down safely but dozens were trapped on the peak.