Astronomical Virtual Observatories (VOs) are emerging research environment for astronomy, and 16 countries and a region have funded to develop their VOs based on international standard protocols for interoperability. The 16 funded VO projects have established the International Virtual Observatory Alliance (http://www.ivoa.net/) to develop the standard interoperable interfaces such as registry (meta data), data access, query languages, output format (VOTable), data model, application interface, and so on. The IVOA members have constructed each VO environment through the IVOA interfaces. National Astronomical Observatory of Japan (NAOJ) started its VO project (Japanese Virtual Observatory - JVO) in 2002, and developed its VO system. We have succeeded to interoperate the latest JVO system with other VOs in the USA and Europe since December 2004. Observed data by the Subaru telescope, satellite data taken by the JAXA/ISAS, etc. are connected to the JVO system. Successful interoperation of the JVO system with other VOs means that astronomers in the world will be able to utilize top-level data obtained by these telescopes from anywhere in the world at anytime. System design of the JVO system, experiences during our development including problems of current standard protocols defined in the IVOA, and proposals to resolve these problems in the near future are described.