There is a tool that can convert JPGIS data which are in xml format into shapefile data. The tool is named ksjtool, and you can choose between (1) 32Bit or (2) 64Bit, as you can see from the image below:
After downloading the file, unzip ksjtool, and install it. Then, open the ksjtool, and you will have two inputs, as you can see in the image below:
(1) Input the xml file;
(2) Input the name of the directory in which the output shapefile will be written;
Then you will have two buttons at the lower right corner:
(3) The upper button is to "Execute the conversion", and
(4) The lower button is to "Close the tool".
I hope this can help.