The alert did not cause widespread panic, but briefly disrupted public transport.
According to the JMA, the error stemmed from an anomaly in calculating the earthquake’s epicentre.
The estimated magnitude was based on an incorrect assumption that the epicentre was about 680 kilometres farther from Japan than it actually was, the weather agency said.
Japan is haunted by the memory of a massive 9.0-magnitude undersea quake in 2011, which triggered a tsunami that killed or left missing around 18,500 people and wrecked the Fukushima nuclear plant.
A 9.9-magnitude tremor would have released about 22 times as much energy as the 2011 quake, according to local media.