The organisations will perform preclinical and Phase I trials on drug candidates that are among the aminopyrazole class of compounds.
The Global Health Innovative Technology Fund (GHIT), a public private partnership fund, will sponsor the project and will donate around JPY600m ($5.59m).
The primary objective of the programme is to deliver an orally active, safe, effective, short-course, field-adapted drug that can be given along with another oral formulation to potentially avoid resistance.
The organisations plan to build alliances and develop new approaches to improve access to medicines for the development of neglected tropical disease treatments.
The Neglected Tropical Diseases Drug Discovery Booster project was also launched by the organisations in 2015 to boost drug discovery targeting leishmaniasis and Chagas disease.
Transmitted through sandfly bites, VL is the most serious type of leishmaniasis, and affects more than one billion people in more than 90 countries.
the disease is characterised by fever, weight loss, spleen and liver enlargement and anaemia, and leads to nearly 30,000 deaths per year.
Takeda and DNDi previously partnered in July 2015 in the Lead Optimization Programme aimed at establishing the best aminopyrazole compound to develop a new drug for VL.
Takeda has also signed an agreement to sell its Brazil-based subsidiary Multilab to the local medical equipment company Novamed. Multilab is involved in the research, development, manufacture and sale of pharmaceutical products.