Phanerogams Section aims to document flowering plants of Nepal and publish them in the form of fascicles, catalogues, local and regional floras that support to publish Nepal Flora. In this connection, the section continues to organize plant expedition to various parts of the country, identify and preserve them in the form of herbarium. Until to date, it has supported to publish many Flora books like 'Flora of Kathmandu Valley, 1986,' 'Flora of Phulchoki and Godawari 1969, 1974,' 'Flora of Langtang, 1976,' 'Phanerogams of Nepal, 2001,' 'Catalogue of Nepalese Flowering Plants-I, 2010,' 'Catalogue of Nepalese Flowering Plants-II, 2011,' 'Catalogue of Nepalese Flowering Plants-III, 2012,' 'Catalogue of Nepalese Flowering Plants-Supplement 1, 2015', several fascicles, manuals and keys and so on. This section also provides plant identification services to clients, students and researchers. Here, the herbarium specimens have been according to G. Bentham and J.D. Hooker (1862-1883) system of classification.

Digitization is the recent vital work that aims to digitize herbarium specimens. It includes preparing high resolution scan of herbarium with barcode, color chart and scale and maintaining a database.  More than 9,000 specimen sheets have been digitized so far. This is a pioneer work in South Asia. After completion of the work, botanists or researchers may have opportunity to access the specimens from any part of the world. Besides, it will help for long term preservation of the specimens as it protects the valuable information on herbarium sheets that may be lost in the event of natural disasters (earthquakes, fire etc) and physical destruction during specimen sheet handling as well.

Cryptogams Section conducts research on Algae, Fungi, Lichen, Bryophytes and Pteridophytes. The Mycology unit documents fungi including mushrooms found in the Nepal. It has published 'Catalogue of Fungi Preserved in National Herbarium and Plant Laboratories, 2014' describing more than 387 species. In Pteridophyte unit, the herbarium specimens are arranged basically with Kramer and Green (1990) system of classification. The recent publication-Fern and Fern Allies of Nepal Vol- I, 2015 has documented 580 taxa of fern and fern allies.

Economic Botany Section aims to document wild plants of economic importance. It has a museum where more than 700 plants specimens of various uses have been maintained for disseminating knowledge to the visitors. Besides, it carries out economic mapping and ethno botanical studies on economic plants.

Ecology and Environment Section aims to investigate the underlying factors that control distribution and diversity patterns and quantitative analysis of plants vegetation and ecosystem.

Cytology Section aims to develop identification procedures based on the size, number and type of chromosomes.

Plant Genetic Resources Section was known as 'Arboretum Section' before. It has many plants species of the country which are becoming threatened due to various anthropogenic factors. It includes indigenous and exotic live plants that have been conserved by in-situ and ex-situmethods.

Tissue Culture Section is the first Tissue Culture Laboratory in Nepal that had been established in 1976. Tissue culture is a tool to propagate rare and endangered plant in the enormous amount. It can produce superior quality of plant clones, free from diseases with meristem culture. The institute has developed protocol of over 116 species including ornamental, vegetable, tree and fruits. This section has also conserved germplasmof rare, endangered and endemic plant species.

Anatomy Section helps mainly for taxonomic identification, detects adulteration in wood, timber, fiber and suggests whether or not the wood is useful for the given purpose. It continues to serve to identify species from the wood samples for both academic and judicial procedures. Now, there are more than 200 wood samples in 'Xylarium'. It has published 'Wood identification manual of important timbers of Nepal - 2012'. In addition to this, emphasis has been given to dendrochronological study and climate change impact on high altitude plant species.

Medicinal Plant Section attempts to document, domesticate and develop agro technology for the Medicinal and Aromatic Plant species (MAPs). Besides, it conducts feasibility study for their commercialization.

Floriculture Section that develops cultivation and propagation technology of wild, native ornamental plants for commercialization. However, preference is given on the indigenous plants (Bergenia ciliata, Berberis nepalensis, Hypericum perforatum, Rhododendron arboreum and Reinwardtia trigyna).

Plant Protection Section has established to study about plants and their related diseases.

Plant Breeding Section has been established to increase quality and productivity of economic plants by artificial pollination, chemical treatments and radiation.

The Library is one of the best libraries in Nepal for botanical information especially for the Flora. It has a collection of 3100 books and 2100 copies of important journals.

The Administration Section looks after the routine works on personal administration of 43 staff. Out of 43, 18 are Technical Officers (Botany) belonging to 12 Sections, one Administration Officer and one Account Officer, leaded by one Senior Research Officer (Gazetted Second Class/Technical/Botany). The financial administration is the responsibility of the Account Section.