Mani, 45, also a singer, was undergoing treatment for liver and kidney diseases at the Amrita Institute of Medical Sciences.
Mani, who was admitted to the hospital two days ago, passed away at 7.15 PM, the sources said.
Mani, born on January 1, 1971, was an auto rickshaw driver
when he started his career as a mimicry artiste at the famous Kalabhavan, a centre for learning performing arts, here two decades ago.
Entering Malayalam film industry as a comedian, Mani later became an active artiste in South Indian films, including Tamil and Malayalam, especially essaying villain roles.
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His performance in "Vasanthiyum Lakshmiyum Pinne Njaanum" won special accolades from both national and state film award juries.
The Malayalam film industry expressed shock over the actor's untimely demise.
"It is an irreparable lose for us," noted film director Kamal said.
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Meanwhile, Idavela Babu, an office bearer of AMMA
(Association of Malayalam Movie Artists), said Mani's body would be shifted to Thrissur Government Medical College for post-mortem after questions were raised about his death at a young age.
However, police and Amrita Hospital authorities are tight-lipped about the exact cause of death.
Babu said arrangements are being made in Thrissur and his hometown Chalakkudy for his fans and public to pay their last respects.
Prime Minister Narendra Modi tonight condoled the demise of Mani.
"A promising career is cut short. Kalabhavan Mani was multifaceted and popular. Pained by his demise. Condolences to his family and fans," he tweeted condoling Mani's death.