The bus which was on the way from Assam's Silchar went off the road and fell into a gorge at Mawblei, on the outskirts of Shillong at around 4:30 am, the police said.
"We have retrieved three bodies from the site of the accident and we are ascertaining on the number of those who were injured," a police officer on duty said.
While the injured were rushed to Civil Hospital in the city, the police said they have been investigating the cause of the accident.