The incident took place after a crane on which they were sitting on broke apart and crashed to the ground at the EVP Film City near Chennai around 9:30pm on Wednesday.
All three were assistant directors of the film, according to the report.
The dead men have been identified as assistant director Krishna, art assistant Chandran and production assistant Madhu, production house Lyca said in a statement.
"The men were inside the box-like structure on top of the crane when it crashed. It appears they were working on lighting for the shoot," police said.
Director Shankar is making the sequel to the 1996 film, Indian. Police sources said it's not known whether Shankar was at the site when the crane came crashing down.
"Kamal Haasan was at another location inside the complex when the incident happened," said a source who asked not to be identified.
"The accident is cruel. I lost three colleagues. More than my pain, the grief of their families would be immense. I share their sorrow. My deep condolences to them," Kamal Haasan said.
Indian 2, an action thriller, is being seen as Kamal Haasan's film that dabbles in politics. The Tamil Nadu assembly election is due next year.
A case of negligence has been filed against the crane operator and the production manager, the Chennai police said.
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