The Home Minister, who flew in from Guwahati in a special helicopter, met refugees in the camp at the Titaguri High School here.
The visit comes two days after Prime Minister Manmohan Singh visited the district and announced a Rs 300 crore package.
Chidambaram was accompanied by Union Minister of state for Development of North Eastern Region (DoNER) Paban Singh Ghatowar and state Transport Minister Chandan Brahma.
He will meet top district officials and is expected to visit camps in neighbouring Dhubri district where also thousands of people have been displaced in the clashes between Bodos and minorities.
In another development, the state government has shunted out deputy commissioners of Kokrajhar and Chirang districts.
In an administrative reshuffle following the violence in the Bodoland Territorial Areas Districts (BTAD), Kokrajhar DC D Gilfilon and Chirang DC U N Bora have been moved out.
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Rastriya Madhyamik Siksha Abhiyan Mission director Jayanta Narlekar has been named as the new DC of Kokrajhar.
Commissioner of the Guwahati Municipal Corporation Puru Gupta been named as the new DC of Chirang.