Tokyo's NHK World TV reports at least 250 climbers are trapped near the summit of Mt Ontake, with rescue crews on the way.
The Nagano fire department has received several reports of injuries to hikers but has not confirmed their severity.
The JMA raised the alert level for Mt Ontake to three on a scale of one to five. It warned people to stay away from the mountain.
The agency is forecasting further eruptions that may affect nearby residents and is warning of volcanic cinder falling within a 4km radius of the crater.
The volcano straddles Nagano and Gifu prefectures in central Japan and is located about 170km south-west of Nagano.
Japan Airlines said all flights will operate as normal, though the eruption may affect flights out of Tanegashima and Yakushima airports.