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A variety of application results of code clone detection and analysis has been reported. There are many reports of code clone detection and analysis on open source software whereas few reports on industrial systems are open to the public. This paper reports an experience of code clone analysis on a governmental project. In the project, a software system was developed by multiple Japanese vendors. We detected and analyzed code clones in the system, and found that there were many code clones in the project, however we concluded that the presence of the code clones did not have negative impacts on the maintenance of the system because of the following reasons: (1) when different modules are similar to each other in the design document, they also share many code clones in the source code, (2) code clones located in trusted modules, which are libraries maintained by one of the companies.