The two commandos - Kumbinon Mawlong and Dannyboy Nongkhlaw - drowned Saturday afternoon while they were undergoing the water obstacle exercise at the school, run by the Indo-Tibetan Border Police (ITBP), Meghalaya police chief N. Ramachandran told IANS.
He said the ITBP has instituted a court of inquiry into the incident.
Ramachandran said the state government has rushed additional director general of police S.K. Jain to Mahidanda to conduct a probe and submit a report within one week.
Meanwhile, the bodies have been sent for autopsy and will be flown to Guwahati Sunday from New Delhi.
Over 100 Meghalaya police personnel are undergoing special commando training at the CIJW School to fight against the rebels of the outlawed Garo National Liberation Army in the five districts of Garo Hills in western Meghalaya.
The Garo Hills region, which comprises of three districts in the western part of Meghalaya, is home to more than five rebels groups fighting for a sovereign or autonomous homeland for the tribal Garos.
The region, which shares its border with Assam as well as Bangladesh is also being used as a safe haven and hot corridor for various northeast-based militant groups including the National Socialist Council of Nagaland-Isak-Muivah (NSCN-IM), the United Liberation Front of Asom (ULFA) and the National Democratic Front of Bodoland (NDFB).