The famous hill shrine of Kedarnath in Rudraprayag district of Uttarakhand bore the brunt of torrential rains and was covered in mud and slush. About 500 people, including several pilgrims, are said to missing in the area, according to top government sources.
The death toll may rise significantly once water recedes and relief teams are able to access the affected areas.
A portion of the Kedarnath temple compound was washed away but authorities said no damages were reported to the structure itself.
Army Central Command officials said that nearly 6,000 to 8,000 people are stranded in Kedarnath, 2,500 in Hemkund Sahib and around 8,000 in Badrinath.
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Flash floods, cloudbursts and landslips have so far claimed 81 lives in northern India. Thousands have been displaced in Uttar Pradesh where several rivers are in spate.
The death toll in Uttarakhand has reached 52. Rudraprayag district was the worst hit with 20 people dead and 73 buildings, including 40 hotels, along the banks of the Alaknanda swept away in the swirling waters of the river.