Attempts have been made to improve a method of inactivating a Japanese encephalitis vaccine and examine the safety of a vaccine produced by mixing a plural number of vaccines. As a result, a Japanese encephalitis vaccine, which can be stably stored over a long period of time compared with the existing Japanese encephalitis vaccines and has a high safety because of being produced by cell culture, can be successfully produced. Moreover, a similar production method is expected to have a potential to improve the storage stability of other virus vaccines.