More than 50,000 people are stranded after the floods swept away buildings and triggered landslides.
A large number of them are reported to be trapped around the holy town of Kedarnath, located in a valley.
State Chief Minister Vijay Bahuguna has described the floods as a "Himalayan tsunami".
Officials say that the number of dead could exceed 1,000 people, although the exact number will be known only after a survey of the entire region is completed.
Bodies are scattered all around the Kedarnath, in Rudraprayag district, some officials have reported.
Flood-related deaths have also been reported in Himachal Pradesh and Uttar Pradesh states and neighbouring Nepal.
The monsoon season generally lasts from June to September, bringing rain which is critical to the farming output, but this year the rain in the north of India and parts of Nepal has been heavier than usual.
Media reports say military helicopters and the army are mainly targeting Kedarnath, where portions of a famous Hindu temple have been washed away and the shrine is "submerged in mud and slush".
Many visiting pilgrims and tourists in Kedarnath remain unaccounted for, officials say.
Local police chief Ajay Chadha told the BBC that while no-one was stranded in the town itself, thousands remain marooned in the hills that surround it.
"They are being brought down to Kedarnath and will be evacuated tomorrow [Friday] morning," he said.
Mr Chadha said that troops were assisting the rescue operation and were doing "wonderful work".
He said that in one area they had made a rope-bridge, which had been used to rescue at least 1,200 people.
'Unprecedented' Kedarnath temple priest Dinesh Bagwari told BBC Hindi that he heard a loud explosion as a lake above the town burst its banks.
"The floods arrived minutes later and everything was gone in 15 minutes," he said.
"We spent 36 hours without water or food. I saw several hundred people trapped in inhuman conditions. Five of my family members are missing and my 17-year-old son is stranded there."
More than 33,100 people have so far been rescued, as the military takes advantage of clearer weather, but another 50,400 are still stranded, the Uttarakhand home ministry said in a statement released late on Thursday.
"Our priority is to take out the children and women first by helicopter," an Indo-Tibetan Border Police spokesman said.
More than 5,500 soldiers and hundreds of paramilitary and disaster management officials are working to rescue and provide emergency supplies to thousands of tourists and pilgrims stranded in towns and temples, officials say, with 20 helicopters being deployed.
Rescue operations were halted on Thursday morning due to rains and bad visibility, but resumed later in the day after the weather improved.
Chief Minister Bahuguna said the death and destruction in the floods was "unprecedented". Officials say the rains in Uttarakhand have been the heaviest in 60 years.
Prime Minister Manmohan Singh has described the situation there as "distressing" and announced a 10bn rupee ($170m; £127m) aid package for the state.

bbc.com