In 1958, the Central Public Health Engineering Research Institute (CPHERI) was established. It was created by the Council of Scientific and Industrial Research (CSIR). In 1974, after participating in the "United Nations Inter-Governmental Conference on Human Environment" and with its renaming by Prime Minister Indira Gandhi, CPHERI became the National Environmental Engineering Research Institute (NEERI). NEERI has headquarters in Nagpur and five zonal laboratories in Mumbai, Kolkata, Delhi, Chennai, and Hyderabad.
The study for the location of a new municipal solid waste landfill site in Kolkata used the institute's 2005 guidelines.
During the COVID-19 crisis, the institute developed a saline gargling sample method to trace the disease.