Based on the developed low-temperature step-by-step diffusion of impurity manganese atoms, magnetic nanoclusters of manganese atoms were formed in the crystal lattice of silicon with controllable concentration, with specified and reproducible electrophysical parameters. With the help of electron spin resonance, it was proved experimentally that magnetic nanoclusters are formed in p-Si<B,Mn> silicon and consist of four positively charged manganese atoms which are situated in the nearest equivalent inter-nodes around the negatively charged boron atom. Based on the study of electrophysical properties of the material obtained it is shown that in such materials an anomalous Hall effect is observed. Magnetoresistance in silicon p-Si<B,Mn> with magnetic nanoclusters at room temperature was studied and a giant negative magnetoresistance (NMR) Δρ/ρ~300 %, was found, it was shown that with increasing concentration of nanoclusters, NMR value essentially rate.