Police were hunting for two men suspected of firing four shots at Narendra Dabholkar as he was taking a morning walk. Hundreds of students and activists decried the killing in a day-long protest,
The 67-year-old doctor-turned-activist had been receiving death threats for years since he began travelling to hundreds of villages around Maharashtra state to lecture against superstitions, religious extremism, black magic and animal or human sacrifice, according to his friend and fellow activist, Deepak Girme.
Mr Girme said: "He would say he was a medical doctor but that superstition was a bigger disease causing a lot of harm, especially to the poor and the gullible.
"He wanted to expose the people who cheat the poor in the name of gods, who promise false cures for cancer or do black magic to perform so-called miracles."
Activists urged the government of Maharashtra state to pass long-stalled legislation that Mr Dabholkar had worked on to ban such practices.
Mr Girme said Mr Dabholkar's organisation, the Maharashtra Blind Faith Eradication Committee, would continue its work in lecturing about the benefits of scientific attitudes and social cooperation and lifting women from religious subjugation.