Nehwal revealed that the pain started during the All-England Championships in Birmingham earlier this month, where she lost in the final to Spain's Carolina Marin.
"Having some pain in my shoulder hope to recover soon," the Olympic bronze medallist said on Twitter.
However, she later clarified that the pain was "not serious" and that it comes with the territory of being a professional shuttler.
"It is not serious but there is some pain," Nehwal was quoted as saying by Badminton Planet. "While playing I just got it but it happens when you are playing at the highest level."
The India Open Super Series gets underway on April 1 at the Siri Fort Sports Complex in New Delhi.