"Piku" has secured other nods in categories like best director for Shoojit Sircar, Deepika for best actress, best supporting actor for Irrfan Khan and two nods (best film and best male actor) in critics' choice, a release by the organisers said.
The road drama revolved around a hypochondriac old father and his cranky daughter.
This year's frontrunner "Bajirao Mastani", a historical epic starring Deepika and Ranveer Singh, and romantic-comedy "Tanu Weds Manu Returns" come second with six nods apiece.
Both Priyanka Chopra and Tanvi Azmi have been nominated for best supporting roles for the period drama.
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Kangana Ranaut starrer "Tanu Weds Manu Returns" bagged her both best actress and best actress critics' nods.
The sequel's other nominations are for best film, Aanand L Rai for best director, Deepak Dobriyal for both best supporting actor and best actor in a comic role.
Also nominated in the best film category are "Dil Dhadakne Do" and "Bajrangi Bhaijaan".
Siddiqui is also nominated in the best actor in a negative role category besides Darshan Kumar for "NH10", Ronit Roy (Guddu Rangeela) and Manoj Bajpayee (Tevar).
Kanu Behl's "Titli" is nominated in the best debut director category, whose other contenders are Neeraj Ghaywan (Masaan) and Haeshwardhan Kulkarni for "Hunterrr".
The upcoming second edition of Times of India Film Awards is scheduled to take place in Dubai on March 18. The awards ceremony will witness performances by Bollywood celebrities like Varun Dhawan, Jacqueline Fernandez, Kareena Kapoor Khan, Yo Yo Honey Singh and many others.