The MER is in charge of managing two priority axes under the Operational Programme for Human Resource Development. The budget for the first priority axis, that of lifelong learning, amounts to approximately one billion EEK including co-funding by the state. This will provide funding for the development of general and vocational education, youth work, language training, and adult education. The biggest programmes are the Substantive Development of Vocational Education (165 million EEK) and the Adult Vocational Training and Development Activities (130 million EEK). The latter programme will be preceded by the project Vocational Training of Adults in Institutions of Vocational Education, which was launched in 2007 and is funded by the ESF and MER, and which created opportunities of lifelong learning for working adults. Funding will also be provided for the following areas: language instruction for non-Estonians; development of the professional qualification system; e-learning in institutions of vocational and general education; career and study counselling systems; the popularization of vocational education; guaranteeing the quality of youth work; adult education in informal education centres; the popularization of adult education; teacher training and improvement in the quality of the general education system.

The budget of the priority axis of higher education, research and development amounts to 1.8 billion EEK, which includes co-funding by the state and the own funding of the implementers. The biggest programmes include DoRa, which aims at supporting the internationalization of doctoral studies and higher education (500 million EEK, implemented by the Archimedes Foundation) and Mobilitas, which supports research and development in key areas (318 million EEK, implemented by the Estonian Science Foundation).