Carbon nanotube systems can substantially increase their capacity for Li ion uptake, provided that the nanotube interiors become accessible to the ions. We examine theoretically, with ab initio simulations, the ability of Li ions to enter a nanotube interior. While our calculations show that it is quite unlikely for the ions to pass through pristine nanotubes, they are much more likely to enter via large-sized topological defects consisting of at least 9- or more membered rings. It is unlikely that such defects are formed spontaneously, but it may be possible to induce such topological defects by violent non-equilibrium means such as ball milling, chemical means and/or ion bombardment. Indeed, recent experiments on ball milled nanotube samples do report an important increase in the Li ion uptake.