Scientists believe the illness is caused by pesticides and fertilisers.
The FAO is accused by campaigners of encouraging the use of agrochemicals on behalf of multinational companies.
But the FAO strongly denies it is to blame for the spread of Chronic Kidney Disease of Unknown Aetiology (CKDu).
For at least 20 years many Sri Lankans in farming communities have been suffering from a mystery kidney disease – 20,000 are reported to have died while 450,000 are affected.
A few months ago, after a careful study, local and foreign scientists concluded that the excessive use of pesticides and fertilisers using toxic metals – cadmium and arsenic – was the main cause.
A development campaign group, the Swarna Hansa Foundation, has now started a campaign against the FAO, saying it is to blame for “promoting agrochemicals” on behalf of multinational companies.
It is demanding the FAO compensate those affected and has warned that if this is not forthcoming, it will launch a “mass campaign” against both the FAO and the Sri Lankan government.
But an FAO official told the BBC the accusation was false and the organisation was not promoting anyone’s business interests.
An official in the Ministry of Agriculture said the government was doing all it could to reduce the use of harmful farming substances.
A few months ago it banned three major imported agrochemical products.
But the official said the causes of the kidney disease still remained ambiguous and might be linked to the prevalence of hard water in the affected districts.
The campaigners say that the disease is spreading – having started in the northern-central part of the island it is now being detected in the south.
The head of the Swarna Hansa Foundation said that in one village there, 50% of families were affected.