Shahid, 34, however, lost the best actor trophy to Kannada actor Sanchari Vijay.
"And Haider wins five at the national awards. So so so happy. Every one of them so well deserved. Proud. Big grin," Shahid posted On Twitter.
The Kashmir-set modern adaptation of Shakespeare's "Hamlet", starring Shahid in the lead, won best music director and best dialogues honours for film's helmer Vishal Bhardwaj.
Its other three wins were in the categories of best playback singer for Sukhwinder Singh ('Bismil'), best costume design and best choreography.
Shahid is currently shooting his upcoming film "Udta Punjab", which focuses on the drug problem in the state.