Also, even if Java is nominally portable, cross-platform malware is an elusive goal, because malware tends to do things at a quite low level - that is, a level which is very OS-specific.
These are reasons why Java will not look as the best language ever to malware writers. This may help in cleansing a Java-based malware infestation. Java VM implementations come with extensive debugging tools which allow plugging into a running VM and inspecting what happens in it.
Malware usually prefers inconspicuousness. They are optimized for big applications which will use lots of RAM anyway, so any Java code has a large minimal memory footprint.
The existing Java VM implementations are fat. Or a specific sandbox escape bug must be exploited such bugs are discovered regularly, but they are also patched with commendable alacrity. To run native code or access arbitrary files, a Java applet must ask for permission, which entails digital signatures and certificates which may be tracked back to the perpetrator. The Java VM tends to sandbox Java applets. Java is not installed by default in many modern operating systems. The hard parts for Java-based malware are: Java also features a rich standard library which allows it to read and write files in arbitrary ways. Java can actually write a DLL file somewhere (as a bunch of bytes) and load that, so everything native code can do, so can Java. code written in C or whatever, and compiled to a sequence of CPU opcodes) through a standard interface.
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