The FIR was lodged under sections 354 A (sexual harassment) and 506 (criminal intimidation) of IPC, a police officer said, adding no arrest has been made.
Yesterday, Chief Minister Devendra Fadnavis had directed Principal Secretary, Health, Sujata Saunik, to probe the allegations after the woman doctor sent a written complaint to him.
The 26-year-old doctor alleged that Mali asked her inappropriate and personal questions for around two hours in the minister's ante-chamber in March this year.
Mali has denied the allegations. Sources in the ministry said yesterday that he had been asked to go on leave.
The woman submitted a written complaint to police yesterday.
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