What hardware platform are you using? I am planning on providing more "official" support for Android soon with Encog. I plan to look into some optimizations.
Basically, the problem seems to be the speed of the Java math libraries on the Android platform. Other packages have similar issues. You can see more here. Android floating point math performance
I believe the means to make Encog faster on the Android is to make use of the Android NDK or possibly make use of some of the routines from BLAS.