Bahuguna said there was lot of debris around the shrine dedicated to Lord Shiva and it would require at least one year to clear it.
"Kedarnath shrine will remain out of bounds for pilgrims for one year," Bahuguna said.
Parts of Uttarakhand experienced flash floods triggered by incessant rains over the past three days which has left 150 people dead and thousands others, most of them tourists and pilgrims, stranded.
The Prime Minister and UPA chairperson Sonia Gandhi undertook an aerial survey of the rain-affected regions.
Pictures of the Kedarnath temple, one of the holiest of the Hindu shrines, in Wednesday's newspapers had raised concerns over the safety of the shrine.
Located in the Himalayas at a height of 3584 meters near the Chorabari glacier, the Kedarnath temple is a popular destination for Hindu pilgrims from all over the world.