Charge dissipation and self focusing limit in high current density ion beam transport through micro glass capillaries are investigated. It is demonstrated that ion beams can be guided efficiently (capillary exit diameters; straight capillary (SC): 860 µm, tapered capillary (TC): 500 µm, 300 µm, 200 µm, 110 µm, 45 µm and 20 µm) with minimal loss of beam current, and thereby transport of ion beams (J ~ 600 Am −2 ) become possible, over a tilt angle of 5° from the incident beam axis. The investigation reveals the existence of a lower limit on the capillary size, below which Coulomb repulsion of the beam's space charge dominates over the inward radial forces of the charges that get smeared on the capillary inner wall, and the beam can no longer self-focus, although the beam may be transported. Beam size compression at the capillary exit by as much as 81% could be achieved. A theoretical model validates the result and the self focusing factor tends to 1 for smaller capillary outlet. Charge dissipation is evaluated during a hysteresis cycle of beam current with ion energy, and it is found that maximum charge dissipation occurs for the 300 µm capillary outlet (~6 × 10 13 electronic charge). A nonlinear behaviour of the beam spot diameter with the capillary outlet is observed. Particle in cell (PIC) simulations are performed to interpret results.