"Politely disagree with the views expressed by Swami Swaroopananda ji about women's entry in Shani Shingnapur temple will bring ill luck to them and give rise to crimes against them; and attributing drought situation in Maharashtra to Shirdi Saibaba worship," Naidu said on Twitter.
On Sunday, the Shankaracharya had waded into a controversy by saying that entry of women in the Shani Shingnapur temple will lead to rise in crimes against them like rape.
Swaroopanand also said the prevailing practice of worshipping Sai Baba in the temples of Maharashtra was responsible for the drought in the state.
The comments had kicked up a controversy.
A 400-year-old ban on entry of women into the shrine's core area was lifted by the temple trust last week following advocacy group Bhoomata Brigade's agitation against gender bias and the Bombay High Court order upholding women's equal rights to worship.