Bahuguna laid wreaths on the dead bodies of Captain Jagjit Singh Dhaliwal and technician Abhay Ranjan at the Sahasradhara helipad, official sources said.
The deceased were also given a guard of honour by state police.
The bodies of the pilot and the technician are being sent to their families in Noida and Delhi, sources said.
The Bell 407 helicopter crashed while taking off from Garurchatti in Rudraprayag for Kedarnath in bad weather after apparently hitting a mountain yesterday.
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Yesterday's crash was the third chopper accident in over a month in Uttarakhand during relief operations.
An IAF Mi-17 V5 chopper on a rescue mission had crashed near Guptkashi on June 25, killing all 20 on board.
A private chopper with relief material had met a similar fate on June 21 in Gaurikund area, leaving the pilot injured.