A team of experts, drafted in by the Ministry to examine the study, said there appeared to be errors in the testing procedure and that important data was missing.
The news is a blow to the study's author, Center for Science and Environment, which three weeks ago said its independent lab tests had found between three and five different pesticides in all 57 Coke and Pepsi drinks sampled.
The release of the findings has caused uproar in India, and several states have banned Coca-Cola and PepsiCo drinks from public buildings.
It is the second time in three years that the CSE has released data showing Coke and Pepsi drinks contaminated with pesticides in India.
The government of Karnataka, in southern India, has now filed a lawsuit against Coca-Cola, claiming tests observed by state officials found excessive pesticide residues in some drinks, according to a report Monday by Agence France Presse.
Both firms have repeatedly stated their drinks were safe and paid for newspaper adverts to refute CSE's claims. The groups' shares have largely recovered from an initial dip after CSE published its report.
India is a key emerging market for Coke and Pepsi, containing roughly a sixth of the world's population and a soft drinks sector growing between seven and eight per cent per years.
Coca-Cola said test data from the UK's Central Science Laboratory, affiliated to the UK government, showed pesticide residues in its drinks were below the Indian government's proposed 0.1 parts per billion limit for individual pesticides in fizzy drinks.
The lab also said in a letter, seen by BeverageDaily.com: ""There is no evidence in the (CSE) report that, even if the pesticides were present, the levels were measured with any accuracy".
CSE fought back, saying its lab had used the same methods as many governments around the world, and has the international quality standard ISO 9001:2000.
It has called for the Indian government to implement the proposed limits on pesticides in fizzy soft drinks, drawn up by the Bureau of Indian Standards.