The boundary element method (BEM) is a useful tool in Diffuse Optical Imaging (DOI) when modelling large optical regions whose parameters are piecewise constant, but is computationally expensive. We present here an acceleration technique, the single-level Fast Multipole Method, for a highly lossy medium. The enhanced practicability of the BEM in DOI is demonstrated through test examples on single-layer problems, where order of magnitude reduction factors on solution time are achieved, and on a realistic three-layer model of the neonatal head. Our experimental results agree very closely with theoretical predictions of computational complexity.