I had this same problem and found the fix for it two minutes ago.
I'm using Fedora Core 1.
What I did was go to $JAVA_HOME/lib as root and give the following commands:

./unpack tools.pack tools.jar
./unpack rt.pack tools.jar

After that I ran
java -version
to make sure that java was working right and it did. I don't know a lot about java so I don't know how it works, but it worked for me. I hope it works for you.