The permission is not associated with your program but with who (which account) runs this program, if it's being executed by a system account with administrator privileges then the program will have the power to perform I/O operations everywhere.
In linux you can grant 'sudo' access to non-root users, you can check if that would be an option for you, however, it seems like a risky scenario, you might want to study this use case and consider specifying the exact permissions you need based on your needs
If you are not sure who's running this program, you can verify the java process:
- Search for a java.exe in your Windows environment
(http://technet.microsoft.com/en-ie/sysinternals/bb896653.aspx)
- Run
ps fuxa | grep java
in you linux terminal