In this paper, we demonstrate a technique for highly stable atom-tracking control of a scanning tunnelling microscope (STM) tip by referring to an atomic point on a regular crystalline surface. We also demonstrate an atomic encoder using 'atom-by-atom' step control along a crystalline axis. A graphite crystal, whose lattice spacing is approximately 0.25 nm, was utilized as the reference material. To enhance the stability of the atom-tracking control in the presence of external disturbances, a robust controller, consisting of an integrator, a tracer and limiter units, was developed. Experimental results show that the proposed method has high capability for maintaining the atom-tracking control without any jumping of the STM tip to adjoining atoms, even in a noisy environment. This method was also applied to atom-step control of the STM tip by referring to a specific crystalline axis. Atom-stepping control along a crystalline axis over a range of 200 atoms and at a rate of 10 atoms s⁻¹ was performed and demonstrated without missing the atomic array.