The simplest way to do that, is by multiplying the object's rotation matrix with a none-uniform scaling matrix. Something like
Matrix m=new Matrix();
m.set(1,1,2f);
cylinder.getRotation().matMul(m);
However, this affects lighting in a way that might look strange. Just give it a try and see if it's sufficient. If it's not, please report back here and we'll find another solution.