The IED went off in a two-storey building next to the Raj Bhavan compound at around 5:30 am but there was no report of any casualty in the blast, the officer said adding the area has been cordoned off.
The blast took place hours before the commencement of the Manipur Assembly session today.
The session began as usual.
No group has claimed responsibility for the blast so far.
In a fatal attack on an army convoy in Chandel district of the state earlier this month 18 soldiers were killed.