The awards, which were spread out in Tamil, Telugu, Bengali and Marathi languages, saw Bollywood movies like "Pink", "Neerja" and "Dangal" score in key categories.
"Rustom", a court room drama directed by Tinu Suresh Desai, is loosely based on the 1959 Nanavati murder case.
Akshay, 49, took to Twitter to express his gratitude over his surprise win.
"Thank you is a very small word right now but I don't know how else to express how I am feeling right now... 'Rustom' was a very special role to play. Being able to wear the uniform of Indian Navy itself is a huge honour, even if it's just for a role," Akshay said in a video message to his fans.
"Neerja", directed by Ram Madhvani, was named the best Hindi film. It is based on the 1986 hijacking incident during which flight attendant Neerja Bhanot was killed by terrorists while saving passengers.
"This is huge. Here is to Neerja Bhanot and her family," Madhvani told PTI.
Amitabh Bachchan-starrer "Pink", a female-centric court room drama, won the award for best film on social issues.
Producer Shoojit Sircar dedicated the award to his team and Bachchan, saying it would not have been possible to make the female-centric drama without the actor's support.
Ajay Devgn's "Shivaay" won the best special effects.
The 11-member jury, headed by Akshay's frequent collaborator, filmmaker Priyadarshan, named Surabhi C M as the best actress for her role in Malayalam film "Minnaminungu-The Firefly".
"I never expected this award. I expected only a jury mention. I am extremely happy and stunned," Surabhi, who is away in Muscat as part of a programme, said.
"Kasaav", this year's best feature film winner by Sunil Sukhtankar and Sumitra Bhave, revolves around the issue of depression and environment conservation.
"'Kasaav' got the best film award which is a great thing but another point of happiness is that the film deals with the theme of depression. The award definitely gives a boost to Marathi cinema. It is a proud moment for us," co-director Sunil Sukthankar told PTI.
Besides "Kasaav", Rajesh Mapuskar won the best director award for his film "Ventilator". The movie, produced by actress Priyanka Chopra and her mother Madhu, won three awards.
"Ventilator" also won the best editing and the best final mixed track award.
The best adapted screenplay went to "Dashakriya", which was also chosen as the best Marathi film, while its star Manoj Joshi was named the best supporting actor.
Malayalam film "Maheshinte Prathikooram" won the best original screenplay award and the best dialogues went to Telugu movie "Peli Chuplu".
Special Jury award went to Mohanlal for his notable work in films like "Pulimurugan", "Janatha Garage" and "Munthirivallikal Thalirkkumbol".
Indira Gandhi Award for the best debut film of a director went to Bengali movie "Alifa" by Deep Choudhary.
Tamil movie "24" won for the best cinematography and production design.
The awards for the best male playback singer went to Sundharayyar for Tamil movie "Joker" for the song 'Jasmine E', while the best female playback singer award went to Iman Chakraborty for 'Tumi Jaake' from the Bengali movie "Praktan".
The best child artist award was shared by Adhish Praveen, Nur Islam, Saimul Alam and Manohara K.
Peter Hein of "Pulimurugan" was named the best stunt choreographer, while Jayadevan won the best sound designer award for the Malayalam movie "Kaadu Pookunna Neram". Raju Sundaram won the best choreography award for his work in Telugu film "Janatha Garage".
"Mahayodha Rama" won the best animation film award while "Loktak Lairembee" won the best environment conservation /preservation.
Hindi films "Kadvi Hawa" and "Mukthi Bhawan" received special mentions.
The National Film Awards will be handed out to the winners by President Pranab Mukherjee in a ceremony on May 3.
Disclaimer: No Business Standard Journalist was involved in creation of this content
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