Police said they were not treating the death as suspicious after finding his body on Monday in Essex, northeast of London.
"We attended and, sadly, a 49-year-old man was pronounced dead at the scene. His next of kin have been informed," Essex Police told AFP.
"The death is not being treated as suspicious and a file will be prepared for the coroner."
The Prodigy issued a statement calling Flint a "true pioneer, innovator and legend", Britain's domestic Press Association news agency reported.
Heavily tattooed and topped with a bleached mohawk, Flint helped turn The Prodigy into one of the most influential groups to emerge from the underground rave scene.
Their biggest hits included "Firestarter" and "Smack My Bitch Up", which merged elements of drum and bass, heavy metal and techno.
"There was a real determination for it to have zero compromise," Flint told AFP in 2015.
"There really needed to be an antidote to the DJ scene, which made it quite brutal."
True pioneers of electronic music, The Prodigy still headline some of the biggest concerts around the world 29 years after their first hit.