The move follows a report produced by Elsevier for the Department for Business, Innovation and Skills last year - International Comparative Performance of the UK Research Base - 2011 - which indicated that research papers co-authored by UK researchers and international collaborators received twice as many citations as papers whose authors were from a single UK institution.
The precise areas to be jointly funded by the MRC and the Japan Science and Technology Agency will be thrashed out at a joint workshop with researchers, which will be followed by a joint call for proposals.
The initial focus of the collaborations will be neurodegenerative disorders and mental health.
Mark Palmer, head of international strategy at the research council, said: "The MRC is keen to ensure that the best UK researchers are able to work with the best researchers elsewhere in the world to accelerate progress in medical research.
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"Japan is one of the world leaders in biomedical research and...we anticipate that this agreement...will be mutually beneficial and lead to high-quality research."
Meanwhile, Research Councils UK and the Chinese Ministry of Science and Technology have launched a joint call for research proposals in healthy ageing populations plus energy and food security.
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The programme, which is aimed at boosting bilateral research collaboration between the UK and China, will see RCUK and the Chinese ministry each put up £1 million to finance the collaborations.
The projects funded will be eligible for up to £200,000 from each source.
RCUK set up an office in China in 2007 with the aim of promoting collaborations. It hopes that the co-funding programme will help develop a "feasible and sustainable cooperation mechanism" that can be replicated in future projects.
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