Red alert has been issued at Subhashini and Dolphinpara tea estate areas as the Torsha river swelled due to heavy rainfall in north Bengal.
Yellow alert was issued at Joygaon and Hashimara as well as in various place on the banks of Teesta, Jaldhaka and Raidak rivers flowing through the area, officials said.
With large scale submerging of land being reported, around 5,000 people have been evacuated and provided shelters at three relief camps in Alipurduar district, they said.
The areas submerged include Kumargram, Kalchini, Alipurduar blocks one and two, Madarihat and Hasimara.
Food, drinking water, tarpaulins are being distributed among the affected and evacuations are on, the officials said.
