The main principles of R&D in Estonia are defined in the Organisation of Research and Development  Act (first version adopted in 1997), which stipulates the bases for the organisation of R&D and secures the legal means for the preservation and further development of scientific and technological work as a part of the Estonian culture and economy.

The largest funding instruments that the Estonian Research Council manages are institutional research funding and personal research funding. Institutional research funding enables research and development institutions to fund high-level research and development activities and to modernize and maintain the necessary infrastructure. Personal research funding is funding allocated for the research activities of individuals or research groups.

The funding of post-doctoral research is organized through several programmes, e.g. the national post-doctoral programme (2005-2010), researcher mobility programme Mobilitas (2008-2015) and the ERMOS programme (2010-2014). Mobilitas is funded by the European Social Fund and ERMOS is co-funded by the European Union in the framework of the COFUND scheme.

In the framework of the Mobilitas programme, the Estonian Research Council also funds top researchers who have come from abroad to work in an Estonian research and development institution with the purpose of creating one’s own research group in one of the priority development areas of the Estonian Research and Development and Innovation strategy (RD&I strategy).

International cooperation projects are funded by the Estonian Research Council in the framework of either bilateral (the PARROT programme with France, memoranda with the Russian Humanitarian Scientific Foundation and the US Civilian Research and Development Foundation) or pan-European initiatives (EUROCORES, ERA-NET, ARTEMIS, EMBO).

International cooperation programmes provide various options for funding research cooperation. For example, the Parrot programme offers travel grants for cooperating with French researchers; post-doctoral grants are provided by both the Japanese Society for Promotion of Science (JSPS) as well as University College London (UCL SSEES). New calls for proposals are soon to be expected within the Norwegian research cooperation support scheme.