The Institute has started a 2-year Field Epidemiology Training Programme (FETP) leading to Master of Applied Epidemiology (MAE) degree awarded by the Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, an Institute of National importance under the Government of India.

A learning-by-doing course, the FETP-MAE programme consists of up to 6-months intensive course work at NIE and 18 months of practical field placement for hands-on-experience at the trainee's own field station as well as at selected national Institutes. Opportunities for problem based learning experiences are provided to the trainees. The training is imparted by expert faculty from NIE, external faculty from various ICMR Institutes, Public health experts, Academic institutes of excellence, CDC, Atlanta, Australian National University, Canberra, Australia and WHO. The FETP-MAE programme is provided with sound technical and financial support from WHO. Annually up to 10 scholars are admitted to this programme. In service medical professionals deputed from national or state governments with a minimum of MBBS degree and three years experience are eligible for this course.