It was not clear if Chief Minister Okram Ibobi Singh was the target of the blast.
The IED blast occurred near Moirangkhom bus stand at around 6.30 am in a high security zone.
As per the police, one person died on the spot, while the second succumbed to injuries on way to the hospital.
Some among the injured are reported to be critical.
On Tuesday also, five persons were injured in a blast that hit a market complex in the state capital.
That market complex too was just one kilometre away from the official residence of CMs.