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.
"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.
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.