He said he was happy that the 64th edition of the awards represented a "microcosm" of India and celebrates the diversity of languages, customs, religions and culture.
"Indian cinema and its diversity conveys the underlying spirit of brotherhood, tolerance, acceptance and co-existence. The inherent strength of unity in spite of diversity was our cultural heritage which was inherited through ages," Mukherjee said during the ceremony.
"It is an auspicious occasion to receive this prestigious award. I offer my 'pranams' to my parents and to the Almighty who is everywhere. Thank you to his excellency, the President, honourable ministers and jury members and to all my fans everywhere in India," the 87-year-old filmmaker said.
Akshay was honoured for his portrayal of a patriotic naval officer in "Rustom", a court room drama directed by Tinu Suresh Desai, which is loosely based on the 1959 Nanavati murder case. He received the Rajat Kamal and Rs 50,000.
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C M Surabhi was given the best actress award for her role in the Malayalam film "Minnaminungu-The Firefly". She received the Rajat Kamal and Rs 50,000.
"I am very happy that I have won this award so early in my career. I am thankful to the jury and I am happy that regional cinema is being given its due," Surabhi told PTI after accepting her award.
"Neerja", directed by Ram Madhvani, was awarded 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.
The trio cheered the actress as she went up to the podium to accept the special mention.
Amitabh Bachchan-starrer "Pink", a female-centric court room drama, won the award for best film on social issues.
Bengali filmmaker Aniruddha Roy Chowdhury, who made his Hindi directorial debut with "Pink", said after the success of this film he now wants to make more Hindi films.
Marathi movie "Kasaav" led the regional cinema dominance bagging the best feature film honour and was awarded the Swarna Kamal and Rs 2,50,000 each to the director and producer.
"Kasaav", directed by Sunil Sukhtankar and Sumitra Bhave, revolves around the issue of depression and environment conservation.
"I am happy that Marathi films are getting national recognition. I hope that the audience and the jury keep appreciating the work coming from regional cinema," veteran actor Mohan Agashe, who has produced the film, said.
"It has been a marvellous journey with 'Dhanak'. We began the journey at Berlin Film Festival and it culminated with the National Awards in Delhi. It is not a bad trip to take over the past three years," Kukunoor said.
Ajay Devgn's "Shivaay" won the special effects award.
Mapuskar took home the best director award for his film "Ventilator" and was given the Swarna Kamal and Rs 2,50,000. The movie, produced by actress Priyanka Chopra and her mother Madhu, won three awards.
The best adapted screenplay went to "Dashakriya", which was honoured as the best Marathi film, while its star Manoj Joshi was given the best supporting actor award.
Malayalam film "Maheshinte Prathikooram" won the best original screenplay award and the best dialogues went to Telugu movie "Peli Chuplu".
Actor Mohanlal received the Special Jury award for his notable work in films like "Pulimurugan", "Janatha Garage" and "Munthirivallikal Thalirkkumbol".
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 Nargis Dutt award for the best feature film on national integration went to Assamese film "Dikchow Banat Palaax", while the best popular film providing wholesome entertainment honour was handed out to Telugu film "Sathmanam Bhavathi".
The Indira Gandhi Award for the best debut film of a director went to Bengali movie "Alifa" by Deep Choudhary.
Tamil movie "24" won the best cinematography and production design.
Babu Padmanabha was honoured with the best music direction award for Kannada film "Allama", while there was a tie in the best lyrics category -- Vairamuthu won for Entha Pakkam from the Tamil film "Dharma Durai" and Anupam Roy for "Tumi Jaake Bhalo Basho" from "Praktan".
The best child artist award was shared by Adhish Praveen, Nur Islam, Saimul Alam and Manohara K.
Peter Hein of "Pulimurugan" took home the best stunt choreographer award, while Jayadevan won the best sound designer award for Malayalam movie "Kaadu Pookunna Neram".
Raju Sundaram won the best choreography award for his work in Telugu film "Janatha Garage".
Best costume designer award went to Sachin for the Marathi film "Cycle".
"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.