Nilakanta Das, 45, was killed on yesterday in Jiribam by lightning. The second victim died when a truck skidded into a gorge alongside a slippery mountain road in Tamenglong district.
The heavy rains in the state will continue for the next two days accompanied by strong winds and hailstorm, the weather office said.
For three days, the northeastern region has been reeling under torrential rains.
Reports from rural areas say cabbage and other vegetables have been extensively damaged by hailstorm.
The rains have also caused several flights to be delayed or cancelled. Private bus services have stopped long-distance journeys.
(With inputs from IANS)