You may have to recompile Geant4. G4Java needs a slightly modified and corrected version of Geant4 (see Geant4 Modifications).
You need to check out clhep and geant in parallel. To download geant and clhep type:
svn co svn://svn.freehep.org/svn/sandbox/geant svn co svn://svn.freehep.org/svn/sandbox/clhep
now you need the platform specific binary distribution for clhep from http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/clhep-1.9.html.
Unpack this in clhep/platform where platform is one of "ppc-MacOSX-g++", "i386-Linux-g++" or "x86-Windows-msvc".
Now compile geant by typing
cd geant/source make includes make global cd ..
You can install the specific version for your platform by typing:
make windows make windows-install or make linux make linux-install or make macosx make macosx-install