The army, the National Disaster Response Force (NDRF) and the Indo-Tibetan Border Police (ITBP) are scrambling to evacuate those who are stranded.
State officials said rains were lashing Rudraprayag and once again communication to Tilwada and Gaurikund has been cut off.
More than 500 people are stuck at Gaurikund, but efforts to bring them back to safety had to be aborted following heavy rains in the region, an army official said.
Rains are also lashing Guptkashi, Harsil and Badrinath - places were hundreds and thousands are still stranded.
Eight choppers of the Indian Air Force (IAF) were pulled back from rescue operations following heavy rains and inclement weather in Devprayag, which made flying dangerous and at places impossible.
Owing to heavy rains water levels have once again risen in Alaknanda and Mandakini rivers in the Rudraprayag region. Other parts in the state, including Pithoragarh, Nainital, Champawat, Udhamsinghnagar and Haldwani, have also received widespread rains Monday.
Uttarakhand's Minister for Disaster Management Yashpal Arya said that for now the focus of the state government and other agencies was on rescuing people stranded in various parts of the Char Dham Yatra route.
A cloudburst has also been reported from Thalisain in Paudhi though initial reports said no casualties have taken place.
Army officials who are involved in the rescue operations conceded that rains and inclement weather have slackened the pace of the evacuation and the choppers would only be flying in full force once the weather clears up.
Aerial surveys done by them and eyewitness accounts of people who have come back to safety suggest that more than 15,000 people are still stranded.