Shirmuhammad Yusupov of Uzbekistan's Agriculture Ministry says these poisons are spread by the wind and are causing widespread health problems in the local population.
"Several kinds of toxic salts are spreading from the Aral Sea across the Central Asian region and outside it, and is harming people," he says.
A new study, funded by the NATO Science Program, provides support for the belief that chemicals used on the region's vast cotton fields are linked to alarming rates of cancer in the region.
The study was conducted in collaboration with the Institute of Immunology in Tashkent and Texas Tech University in the United States.
Doctor Spencer Wells of the National Geographic Society in Washington has studied DNA samples taken from residents of Uzbekistan's Karakalpak Autonomous Republic.
"[The study] shows that there is a very high level of what we call 'oxidative stress' in these people. They're being exposed to something which is causing problems in their DNA and their actual genetic code," Wells says.
DNA is the acronym for deoxyribonucleic acid, which encodes genetic information in cells and determines their structure, function and behavior.
The study in Karakalpak shows rates of damage 3.5 times higher than those seen in samples from the United States. The rate increases to five times higher in those farm workers living the closest to the agricultural chemicals.
Wells says high levels of DNA damage could explain the region's abnormally high cancer rates. In particular, residents of Karakalpak suffer from the world's highest rate of cancer of the esophagus.
"This potentially could help to explain some of the health problems that they have, particularly the cancers. We believe it's through exposure to toxic substances in the environment -- pesticides [and] herbicides -- that are being applied to the cotton fields upstream," Wells says.
The poisonous residue in the air affects humans in two ways. It enters both the respiratory system through breathing and the food chain through plants and animals, which are then eaten.
Even more worrying is the possibility that these genetic changes are being passed down to later generations.
"There is a generalized level of genetic damage,” Wells says. “Presumably that is also going to be seen in the sperm and the eggs. So, in theory, these changes could be, in part, transmissible to the next generation."
Wells says he had made a plea for the Uzbek government to re-evaluate the way it cultivates its cotton crop, the country's biggest export earner.
Uzbek officials admit the problem, but say there are no ready alternatives to current agricultural methods.
(Khurmat Babadjanov of RFE/RL's Uzbek Service contributed to this report.)