At least 100 people living in and around the banks of Umkhrah River in the state capital have also been evacuated after the water swelled triggering floods in some areas, they said.
"12-year-old S Thabah and her six year-old sister were killed in Mawdngung village after their houses were washed by landslips," East Khasi Hills district SP M Kharkrang told PTI.
He said three men were rescued in Keatinge road area in the state capital after the wall of their house collapsed.
There were at least seven reported landslips in the district in the past 24 hours with at least five today, Kharkrang said.
East Khasi Hills deputy commissioner Sanjay Goyal said the district administration had evacuated over 100 people living along both its banks after the Umkhrah River has swelled above danger marks and they were rehabilitated at a community hall nearby.