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The shrine, one of the four holy dhams, in Rudraprayag district of Uttarakhand bore the brunt of torrential rains.
About 500 people, including several pilgrims, are said to be missing in the area.
Ukhimath Sub Divisional Magistrate Rakesh Tewari told reporters after his return from Kedarnarth that 50 bodies are lying in areas adjacent to the shine.
"We are right now concentrating on rescuing those who are alive," he said.
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.
The Ram Bada area, a busy spot near the temple, has been completely submerged and was not visible from rescue choppers.
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.
Flash floods, cloudbursts and landslips have so far claimed 131 lives in northern India. Thousands have been displaced in Uttar Pradesh where several rivers are in spate.
The death toll in Uttarakhand has reached 102.
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.
A total of 71,440 pilgrims bound for the Himalayan shrines of Kedarnath, Badrinath, Gangotri and Yamunotri are stranded in Rudraprayag, Chamoli and Uttarkashi districts of Uttarakhand with the famous char dham yatra having been suspended due to massive landslides and damage to the road network.
