"This film was not just any other comedy, it was a satire and I'm glad that the jury found it appropriate for an award like this, " Benegal told.
"I'm glad that the film has been recognised but to be honest I would have been more happy if Boman Irani would have got the best actor award for his role in the film. His performance is fantastic and he truly deserves appreciation for it. But, I'm happy that at least the film got its due."
Directed by Benegal, "Well Done Abba" is a political satire that tells the story of Armaan Ali (Boman), a driver working in Mumbai, who takes a month's leave to find a groom for his daughter but only returns after three months to find himself sacked.
Produced by Big Pictures, it also stars Minissha Lamba and Sammir Dattani in pivotal roles.
This is not the first time that Benegal has received a National Award.
When asked of the 75-year-old, who has won the prestigious award seven times, how does it feel to get another one, he said: "An award is an award and it's always nice to receive it."
Was he expecting one for "Well Done Abba".
"No I was not expecting one for the film at all, " he said.