Hidayat, who is Saina's IBL team mate in Hyderabad Hotshots franchise, had complained of unfair treatment to foreign players by the league organisers.
Hidayat was bought for US$ 15,000 at his base price and the Indonesian felt he deserved much more.
- Jwala Gutta ready to battle pain to play
Saina, however, said Hidayat should realise that he was a retired player, a comment which did not amuse Jwala.
"Taufik Hidayat is one of the greatest players....and I don't think u can dismiss his views just because he has "retired" from the game!!!!," wrote Jwala, who plays for Delhi Smashers, on her Twitter page.
"I don't know how anyone can talk about him in such manner......without giving him and his stature any respect...it's absolutely sad!!!!," she said.
Jwala did not name Saina in her series of tweets on the issue but in an apparent reference to the Hyderabadi, she said that she should understand Hidayat's concern.
"No matter how big u have become in sport I think one should try and ustand what ur fellow players views r And work on it!!!," she tweeted.
"Nobody can take away his achievements....just because he's RETIRED!!!! He is and will always be one of the greatest badminton player!!!!
"And again it's not about money....it's about RESPECT!!!!!"
Image: Jwala Gutta
Photograph: Reuters
PHOTOS: Tendulkar cheers for Mumbai Masters in IBL
IBL: Saina Nehwal unhappy over 'wrong' line calls
Saina slams Hidayat for criticising Indian Badminton League
IBL: Delhi Smashers fight back to beat Hyderabad 3-2
IBL: Jwala Gutta ready to battle pain to play