The army resumed helicopter flights to rescue stranded people late Sunday after rain stopped and dense fog lifted in the Himalayan region, Brig. Uma Maheshwar said.
Thousands of people were still stranded in high mountain passes in the temple town of Badrinath and rescue efforts were concentrated on getting them to safety.
Troops built makeshift bridges at several places, Maheshwar said.
Despite poor visibility, more than 2,000 people were transported by helicopter to relief camps in the state capital, Dehradun, said Priya Joshi, an air force spokeswoman.
India's national disaster response force used drone aircraft to locate survivors in remote areas that remained inaccessible.
Hundreds of thousands of devout Hindus make a pilgrimage to Uttarakhand, visiting four of Hinduism's holiest shrines in the state during the summer months. The tourists usually head down to the plains before the monsoon breaks in July. But this year, early rains caught hundreds of thousands of tourists, pilgrims and local residents.
The crisis began when torrential rains washed away homes and roads and triggered landslides that cut off communication links with large parts of the state nearly a week ago.
State Chief Minister Vijay Bahuguna told reporters late Saturday that the death toll had reached 1,000.
About 10,000 army and paramilitary troops, members of India's disaster management agency and volunteers have taken part in six days of rescue and relief efforts. The army has rescued more than 80,000 people by road and air, said Amit Chandola, a state government spokesman.
More rain was expected in the worst-hit Chamoli and Uttarkashi districts over the next few days, said Anand Sharma of the state's meteorological office.
Sharma said the rains in Uttarakhand were the heaviest in nearly 80 years.
In the small town of Gauchar, where the army has set up a camp for those rescued from the temple town of Kedarnath, anxious pilgrims waited for word about relatives yet to be rescued by army helicopters.
"I'm waiting to hear from my daughter and her husband," sobbed Indu Bal Singh, 65, who became separated from her daughter, son-in-law and two grandchildren. Singh was among a group of pilgrims who were rescued first because of her age.
Singh, who has waited two days, refused to return to her home in the eastern Jharkhand state until she is reunited with her family. "I won't move from here until I hear they are safe," she said.
Across India, volunteer groups and ordinary citizens were contributing clothes, food, blankets and money for residents of Uttarakhand whose homes have been washed away by the floods.
The United States will provide $150,000 in emergency relief to families living in remote areas of the state, U.S. Ambassador Nancy J. Powell said Sunday.
"We are deeply saddened by the tremendous personal loss and the damage to houses, public buildings, temples, roads, and bridges, as well as safe drinking water sources, livestock, and agricultural land," Powell said.