The decline in the number can be attributed to deaths due to drowning during floods and to speeding vehicles on National Highway 37.
Forest officials, however, said that there was not much cause for concern as the breeding season of the animal begins in December and the population would again see a rise.
The census was conducted in five ranges with Kohora accounting for 393, Bagori 260, Agratoli 125, Burapahar 52, and six in the Northern Bank.
The enumeration was carried out by the Forest Department, with support from the Wildlife Trust of India and ONGC. Swamp deer was found exclusively in the Kaziranga National Park, but recently about six of these species were spotted in the Manas National Park, forest officials said.