I\'m using the standard ConsoleHandler from java.util.logging and by default the console output is directed to the error stream (i.e. System.
Have a look at the docs and source for ConsoleHandler - I'm sure you could easily write a version which just uses System.err instead of System.out. (It's a shame that ConsoleHandler doesn't allow this to be configured, to be honest.)
Then it's just a case of configuring the logging system to use your new StdoutHandler (or whatever you call it) in the normal way.