The Olympic bronze-medallist had reached a career best World No.1 last week but owing to her loss in the Malaysia Open Super Series Premier semifinals, Saina dropped a position in the list.
She lost to the reigning Olympic champion Li Xuerui, who regained the top spot.
The shuttler from Hyderabad became the first Indian woman to reach the numero uno position after winning the India Open title last month.
Meanwhile, P V Sindhu, who has not been playing for some time due to an injury, managed to retain her No. 9 ranking.
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In men's singles, Kidambi Srikanth has also maintained his No.4 position to remain the highest-ranked Indian male.
H S Prannoy has also remained at No.14, while Commonwealth Games champion Parupalli Kashyap climbed up two places to be at No.15.
The 2010 Commonwealth Games gold-medallist pair of Jwala Gutta and Ashwini Ponnappa also gained a place to be ranked No.18 in women's doubles.