You may use JNI interface to call functions from a library, in your case ffmpeg library. Here is a basic tutorial of JNI: http://marakana.com/forums/android/examples/49.html
To put simply, JNI is the bridge between your Java code and C code.
In order to call ffmpeg as in command line from your Java code, You may include ffmpeg.c (and other needed files) into your jni interface (under jni directory) and compile it along with your other jni code, so that you may call ffmpeg's main function with arguments just like the command line.