Monday’s federal court decision came on the same day that Maoist guerrillas joined a nationwide protest against the two US-based beverage companies.
Delhi High Court Judge B.D. Ahmed told India's additional Solicitor-General K K Sud to test samples of Pepsi and Coke in state-owned laboratories and report back with the results within three weeks.
The court ruling was announced after an appeal by Pepsi's Indian branch seeking an "independent evaluation" of damaging pesticides-in-cola allegations levelled last week by India's Centre for Science and Environment (CSE) non-governmental organisation.
Pepsi argued the CSE laboratory that conducted the testing was not accredited and that the methodology in preparing the study itself was "suspect."
The CSE stunned India's 500-million-dollar soft drinks industry last week with charges that 12 leading domestic and international brands including Coke and Pepsi contained pesticides up to 45 times more than European norms.
The parliament in New Delhi subsequently took the two beverages off MPs' canteen menu, and in a rare sign of political unity, parties of all colours joined together in a campaign which led to smashing Pepsi and Coke bottles.
Coca-Cola has also come under fire for allegedly giving contaminated waste as "organic fertiliser" to Indian farmers in the southern state of Kerala.
A study by the Kerala State Pollution Control Board (PCB) released on Wednesday said there were high levels of cadmium in the sludge, with 201.08 milligrams per kilogram. The permissible World Health Organisation (WHO) limit is 50 milligrams per kilogram. Coca-Cola denies the charge.
The latest to join the anti-fizz drive were outlawed Maoist rebels in eastern Jharkhand state, who set Friday's national independence day as its unilateral deadline for the two firms to wind up their sales in the region.
“The demand has come from the People's War Group, which has also asked the local population neither to buy, sell or drink Pepsi and Coke," a police spokesman from Jharkhand's state capital Ranchi said.
The guerrillas hold sway in 14 of mineral-rich Jharkhand's 18 states.