Consumer prices decreased by 7.2 percent between September 2012 and September 2013.
The National Bureau of Statistics said the annual inflation rate for September went down 17 percent in Wau and 8.9 percent in Malakal and increased 0.3 percent in Juba.
Cheaper food, soft drinks and furniture were the main reason for the fall in prices.
Between August and September prices increased by 3.2 percent.
By regions, Juba registered a monthly inflation hike of 14.1 percent while goods were 1.9 percent cheaper in Wau and 1.8 percent in Malakal.