Being the core activity of the Institute, research is organised into specialist subject divisions, which have evolved over time since inception from eight divisions to the present fourteen divisions, namely:

 Agronomy
 Chemistry
 Plant Physiology
 Plant Pathology
 Plant Breeding
 Entomology
 Biochemistry
 Agricultural Engineering Research
 Production Engineering
 Statistics & Computer
 Agricultural Economics
 Agricultural Extension
 On-farm Adaptive Research
 Tissue Culture & Biotechnology

For effective co-ordination of work in the various research divisions, research has now been organized on programme basis, as follows:

 Oil palm programme
 Coconut programme
 Raphia programme
 Date programme
 Shea Programme
 Product Development and utilization
 Tissue Culture & Biotechnology
 Economics and Extension programme

Each programme is headed by a Programme Leader, who may not necessarily be Head of a Research Division. The research programmes and divisions are further organised into departments as follows:

 Biology and Crop Production Department
 Technology Department
 Economics and Extension Department.