Officials said the incident took place at a labour camp near Umiam Lake around 5 AM during heavy rain, which continued since last night.
Two teenaged girls and a 25-year-old man were killed while two women went missing in the landslide, a district disaster management authority official said.
Nine others were injured in the incident, the official added.
The official said efforts were on to clear the debris and the injured have been referred to NEIGRIHMS, Ganesh Das Hospital and Shillong Civil Hospital.
Meanwhile, Met department officials confirmed onset of the south west monsoon in the north eastern region.