The Royal Swedish Academy of Sciences said the two researchers had made key contributions to experiments showing that neutrinos change identities as they whiz through the universe at nearly the speed of light.
Neutrinos are miniscule particles created in nuclear reactions, such as in the sun and the stars, or in nuclear power plants. There are three kinds of neutrinos and the laureates showed they oscillate from one kind to another, dispelling the long-held notion that they were massless.
Kajita, 56, is director of the Institute for Cosmic Ray Research and professor at the University of Tokyo. McDonald, 72, is a professor emeritus at Queen's University in Kingston, Canada.
The winners will split the 8 million Swedish kronor (about USD 960,000) prize money. Each winner also gets a diploma and a gold medal at the prize ceremony on December 10.
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Kajita and McDonald made their discoveries while working at the Super-Kamiokande detector in Japan and Sudbury Neutrino Observatory in Canada, respectively.
McDonald told a news conference in Stockholm by telephone that the eureka moment was when it became clear that his experiment had proven with great accuracy that neutrinos changed from one type to another in traveling from the sun to Earth.
Asked how he felt when he realised today that his work was suddenly going to receive the world's focus, McDonald said, "It's a very daunting experience, needless to say."
The University of Tokyo said in a statement congratulating Kajita that he was one of the students of 2002 Nobel physics winner Masatoshi Koshiba, who also has contributed to Japan's neutrino research.