The state's disaster management authority said some 50,000 people were sheltering in 168 relief camps across rain-soaked state, with others staying with family or friends, AP reported on Tuesday.
Most of the flooding was caused when rivers, including the Brahmaputra and its tributaries, overflowed their banks. At least 1,600 villages were affected, with the worst-hit in Dibrugarh district.
Some of the 21 killed were washed away in rivers, including a mother and son swept downriver in the raging Fessa.
Wild animals including some 2,500 endangered one-horn rhinos have moved to higher ground in Kaziranga National Park.