The incident occurred near Pakua around 9.30 pm when the bus was on its way from Malda to Bamangola.
Shots were fired from outside towards the bus when it was passing by '11 Mile' locality, injuring two passengers.
The injured were being taken to Malda Medical College and Hospital, sources said.
In areas like Pakua and Bamangola, the ultras of the Kamtapur Liberation Organisation (KLO) were active, the sources said.
Suspected KLO activists carried out a blast in a moving bicycle near Jalpaiguri town in north Bengal, killing five persons and injuring nine others last evening.
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