The notice to the two companies was issued after a study released this week said their drinks contained unacceptable levels of insecticides.
The companies have four weeks in which to respond, the report said.
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The court issued the order in response to a public interest lawsuit that contended the drinks contain harmful ingredients.
The study, published by the privately-funded Centre for Science and Environment (CSE) on Wednesday, found that 11 drinks sold by the two US companies contained high levels of pesticide residues.
Citing the report, Indian MPs on Thursday called for a ban on the sale of Coca-Cola and Pepsi, which enjoy a virtual monopoly on cola sales in India.
"These companies are playing with the lives of millions and we can't ignore such warnings any more," said Vijay Kumar Malhotra of the main opposition Bharatiya Janata Party which later staged a walkout over the issue.
"The time has now come to ban both Pepsi and Coke," he said.
The US companies joined forces to