Some 3,000 people remain missing in India's flood-ravaged north two weeks after the tragedy, but it is unclear how many of those have been killed, a top state official said Sunday.

About 1,000 people, many of them pilgrims and tourists, are confirmed dead after flash floods and landslides caused by torrential monsoon rains hit the Himalayan state of Uttarakhand on June 15, officials have said.

Thousands of soldiers, backed by military helicopters, have wound down rescue efforts after evacuating more than 100,000 people stranded in the state, which was packed with tourists on pilgrimages to remote Hindu temples and shrines.

"As per information we have received, 3,000 people are still missing," state Chief Minister Vijay Bahuguna told reporters in the state capital Dehradun.

Bahuguna announced that families will receive 500,000 rupees ($8,500) in compensation if their loved ones are still missing after the next 30 days.

Some of those initially reported missing may have returned home or continued with their travels but failed to notify local authorities, officials said.

The exact death toll may never be known because some of the bodies may have been washed away or buried under tonnes of debris, Bahuguna told the Press Trust of India.

A state lawmaker said late Saturday the death toll could cross 10,000 but the figure was rejected as "guesswork" by Bahuguna.

A 200-strong team of specialists is scouring the worst-hit temple region of Kedarnath for bodies, which may still be trapped under debris or swept away by floods and landslides, officials said.

"Clearing tonnes of debris lying in the affected areas and extricating decaying bodies which may be lying under them is our topmost priority at the moment," said state director-general of police Satyavrat Bansal.

Rescue workers have recovered bodies in rivers hundreds of kilometres downstream from the flood zone, underscoring the difficulty of finding all those who perished.

Raging rivers swept away houses, buildings and even entire villages in the state, known as the "Land of the Gods" for its revered shrines.

Medical teams have been deployed to assess the risks to public health after warnings of an outbreak of disease due to contamination from hundreds of bodies found in rivers.

Media reported that state officials were warned in advance of heavy rains and possible landslides in the area.

A senior meteorologist said he had asked the state government to halt pilgrimages in the area before the June 15 disaster over concerns about the rains.

"It is true that on (the) 14th we had started giving warnings of heavy rains," local chief meteorologist Anand Sharma told television channel NDTV in Dehradun.

State Chief Secretary Subhash Kumar said the government had received the weather forecasts but described the warnings as routine.