Para-university institutes: NWO, KNAW and NWO-I
A number of institutes that carry out academically-oriented research do so under the flag of three intermediary organisations: the Dutch Research Council (NWO), the Royal Dutch Academy of Sciences (KNAW) and NWO-I, the Institutes Organiation of NWO.

NWO's mission is to enhance the quality and innovation of fundamental scientific research and to promote the dissemination of research results. 

KNAW is responsible for the quality of science in the Netherlands. The KNAW is responsible for a number of research institutes. The institutes are active in the humanities, the social sciences and the life sciences; one institute works at the interface of science and government policy. The Academy institutes are meant to play a leading role in Dutch and international research. They serve as national centres of expertise, manage unique infrastructures, and provide access to their collections, many of which are world-famous.

NWO-I is responsible for nine institutes in the fields of astronomy, mathematics and computer science, physics, history, marine sciences, law and criminality, and space research.

Institutes for applied research: TNO2 Open Innovation Network 
An import actor is the TO2 Open Innovation Network. It is a flexible network structure aimed at cooperation in undertaking cross sectoral research projects.

The largest institute is TNO, the Netherlands Organisation for Applied Scientific Research. TNO's mission is to make it possible to apply scientific knowledge for the benefit of the innovative capacity of companies and the government. Key TNO research fields are: quality of life, the defence and security of society, advanced products, processes and systems, sustainable use of space and the environment, and ICT and services.
The other four institutes for applied research carry out research and related activities in a specific area: 

• Deltares: research into ports, coastlines, rivers, ocean and inland shipping, water management and the environment;
• The Maritime Research Institute in the Netherlands (MARIN): research into shipbuilding, offshore and ocean engineering;
• The National Aerospace Laboratory (NLR): research into aeronautics and space technology for civil and defence purposes.
• Wageningen University & Research: to explore the potential of nature to improve the quality of life.

Technological Top Institutes (TTI’s)
Six institutes for executing collaborative projects between existing knowledge institutes and industry are in the Technological Top Institutes programme. These instututes carry out research into fields that are relevant to strong R&D-intensive sectors in the Netherlands and specific research topics of international relevance.

• Telematica Institute
• DPI The Polymer Research Platform
• Materials Innovation Institute (M2i)
• Next Food Collective
• lygature pioneering medicine together
• Wetsus European centre of excellence for sustainable water technology

Institutes in agriculture
The Research Institutes of Wageningen University & Research carry out application-oriented and field-based research. They are commissioned by the government, commercial businesses and non-profit organisations. On a research project there is often collaboration between several institutes. Collaboration is often also sought with the university and/or national or international partners.

Ministerial institutes
A steadily declining number of institutes are still under the direct responsibility of ministries. For example:

• The Ministry of Justice and Security has its own internal Research and Documentation Centre (WODC).
• The Royal Netherlands Meteorological Institute (KNMI) is an agency of the Ministry of Infrastructure and Water Management (I&W).
• The Netherlands Institute for Social Research (SCP) and the National Institute for Public Health and the Environment (RIVM) are part of the Ministry of Health, Welfare and Sport (VWS).

Other independent research institutes:

• CE Delft: Research and consultancy agency in sustainability
• Digital Society Institute: Pioneering a humane cyberworld
• EMBL: European Molecular Biology Laboratory
• ESTEC: European Space Research and Technology Centre
• HiiL: The Hague Institute for Innovation of Law
• IB: International Baccalaureate
• IHE Delft: Institute for Water Education
• IPA: Institute for Programming research and Algorithmics
• J.M. Burgercentrum: Research School for Fluid Mechanics
• KB: National Library of the Netherlands
• KIT: Royal Tropical Institute
• KWR: Watercycle Research Institute
• MESA+: Institute for Nanotechnology
• Naturalis: Biodiversity Center
• NEN: Royal Netherlands Standardozation Institute
• Netspar: Network for Studies on Pensions, Aging and Retirement
• NIZO: Food Research
• Nivel: Netherlands Institute for Health Services Research
• NKI: Netherlands Cancer Institute
• Platform31: Knowledge Organisation for the City and the Regions
• Sanquin: Blood Bank
• SIKS: Netherlands Research School for Information and Knowledge Systems
• Techmed: Technical Medical Centre
• TKI Dinalog: Dutch Institute for Advanced Logistics