Bhandarkar received the award with a cash prize of Rs.250, 000 Tuesday from President Pratibha Patil in New Delhi.
"This year, I came across many stories of farmers who had ended their lives to evade the debt trap they were in, " Bhandarkar said in a release issued here late Tuesday evening.
"It was extremely moving for me and hence, I decided to donate the prize money. I always wanted to help the underprivileged and this is an honour to serve society, " he added.
Bhandarkar has chosen the families of Kashinath Dagdu, Prakash Darne and Shamrao Kannake on the basis of "thorough research".
He said: "As my movies always portray a real face of society, I really want to help people by any means."
Bhandarkar has won national awards for his earlier films "Chandni Bar" (2002) and "Page 3" (2005).