The Centre for Science and Environment (CSE) said their investigations revealed that the drinks contain harmful residues, posing a health risk.
A CSE report in 2003 resulted in Pepsi and Coca-Cola strenuously rejecting claims that their drinks were unsafe.
Soft drinks manufacturers have condemned the latest findings.
"Soft drinks are completely safe," the Indian Soft Drink Manufacturers Association (ISDMA) said in a statement on Wednesday.
"The soft drinks manufactured in India comply with stringent international norms and all applicable national regulations."
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