The Japanese Macaque monkeys who were dying at the Kyoto University Primate Center were possibly dying from Simian Hemorrhagic Fever (SHF). Dr. C.J. Peters of the University of Texas Medical Branch stated that there have been outbreaks of SHF in macaque colonies in the US and Russia. The disease among macaques is very contagious but it does not affect humans and other non-human primates.
Source: http://www.promedmail.org (Archived 20100718.2403)