The New Zealand director's short film Two Cars, One Night was nominated for an Oscar in 2005.
Waititi said: "Under my guidance I hope they will find a new passion for the 30-60 second feature film genre.
"I look forward to taking this flailing company in a new direction where they can experience a feeling of success and accomplishment."
Hungry Man director and partner Hank Perlman said: "For Taika, summer is from December to February and winter is from June to August---and that's just the kind of "outside the box" thinking we look for here at Hungry Man."
Clip from Flight of the Conchords, directed by Waititi.