The militants lobbed the grenade at the godown at around 9 pm yesterday.
The godown was guarded by central para military forces at Sangaiporou, about 7 km from here.
The officer in charge of nearby Lamphel police station along with police personnel rushed to the spot and was investigating the incident.
Several militant groups had been making extortion demand on FCI officials for the last few years.
No individual or group has claimed responsibility for the crime.