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The cloudburst was reported at around 5:30 pm.Community kitchens and tents near the cave shrine were washed away.
Rescue operation was immediately launched by security forces disaster management agencies. But due to difficult terrain rescue efforts may be hampered during the night.
J&K's Lt Governor Manoj Sinha said he apprised the Prime Minister and Home Minister about the situation. The Centre has assured all possible help.
Army Helicopters have been pressed into service to shift the injured to hospital.
"Situation is under control, rains are still going on. Looking at the hazard level, the Amarnath Yatra has been halted temporarily due to the area being inundated. If the weather remains normal and makeshift arrangements are made, then the yatra can be resumed tomorrow," said spokesperson of the Indo-Tibetan Border Police or ITBP.
A senior ITBP official said that water came from above and sides of the cave after it rained heavily at the upper reaches.
The injured are being airlifted for treatment.
A cloudburst refers to particularly heavy rain in a short period of time over limited geographical area.
The Amarnath Yatra was briefly suspended earlier this week due to bad weather.
The pilgrimage began this year on June 30 after a 2-year Covid gap. More one lakh pilgrims have offered their prayers at the shrine since then.
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