State Disaster Management Minister Javed Khan said 58,000 people are affected in 150 villages of Alipurduar, Jalpaiguri and CoochBehar.
In Jalpaiguri district, the administration has issued a red alert, officials said.
Among the worst affected areas are Kalchini, Chitmahal, Kumargram, Phulbari and Dabgram.
Khan said they have established 43 shelters in the affected districts where relief material is being provided to those who have been temporarily displaced from their houses due to the flooding.
In Alipurduar, there are reports of breach in some mud embankments.
Not only human beings, but even the wildlife in the forests of Lataguri and Jaldapara have been affected by the flooding, the officials added.