After looking around the net. The only working solution I found is supplied by Bambuser which ported ffmpeg to use in their android application.
Code is here: http://bambuser.com/opensource
Basically you copy the .so files to your jni/lib directory, along with any .h files you might need, create a JNI wrapper through javah, and it works.
EDIT:
Since this post was written a few packaged ffmpeg projects for android surfaced, one of the easiest ones to compile and use is here: https://github.com/guardianproject/android-ffmpeg .
It takes the approach of statically compiling a binary (not a library) that is ran through shell command in run time. Search github for ‘android ffmpeg‘ for forks and related projects.
Did not find a well packaged method based JNI implementation, though.