The study released in Bangkok and Manila said intensive agricultural practices and excessive use of nitrogen fertilisers had polluted artesian wells used for drinking water.
Greenpeace said it sampled water from 30 percent of all groundwater wells from both countries and found nitrate levels above the World Health Organisation's safety limit.
The report said contamination was greatest in those areas that used large quantities of nitrogen fertilisers.
It said the greatest risk of nitrate poisoning was "blue baby syndrome", which occurs in infants given nitrate-laden water, and particularly affects babies under four months. It can cause headaches, stupor, fatigue, coma, convulsions, asphyxia and even death, the report said.
Nitrate-contaminated drinking water can also potentially lead to cancers of the digestive tract and has been associated with non-Hodgkin's lymphoma as well as bladder and ovarian cancer, it added.
"Communities think that the water they drink every day is clean because physically, it doesn't smell bad or look bad. But it is actually laced with nitrates from fertilisers which people don't normally associate with pollution," Greenpeace campaigner Daniel Ocampo said in a statement.
"This report shows that unless governments implement policies to ensure the proper use and application of fertilisers in agriculture, we will lose more of our valuable water resources.
Ocampo called for fertiliser subsidies to be phased out and reduced use of the chemicals.