Massive multiple-input multiple-output (mMIMO) technology is a way to increase the spectral efficiency of machine-type communications (MTC). To exploit the benefits from large antenna arrays, accurate channel estimation through pilot signals is needed. Massive MTC systems cannot avoid pilot reuse due to the enormous numbers of connected devices. We propose a pilot reuse algorithm based on channel charting (CC) to mitigate pilot contamination in a multi-sector single-cell massive MTC system having spatially correlated channels. We show that after creating an interference map via CC, a simple strategy to allocate the pilot sequences can be implemented. The simulation results show that the CC-based pilot reuse strategy improves channel estimation accuracy, which subsequently improves the symbol detection performance and increases the spectral efficiency compared to other existing schemes. Moreover, the performance of the CC pilot assignment method approaches that of exhaustive search pilot assignment for small network setups.