By means of scanning tunnel microscopy the surface morphology of reconstructed Au(001) surfaces has been studied after bombardment with 600 eV Ar ions as a function of dose, in the range of ${10}^{13}$ to ${10}^{16} \mathrm{ions}/{\mathrm{cm}}^{2},$ and the experimental results analyzed in the light of molecular dynamics simulations using a glue potential. At low dose $(5\ifmmode\times\else\texttimes\fi{}{10}^{13} \mathrm{ions}/{\mathrm{cm}}^{2})$ new defects, different from the commonly observed vacancy islands are reported. They appear as depressions 0.06 nm deep, with a characteristic width of 1.44 nm. Bombardment with similar doses of Pt(001) show the same general behavior. Molecular dynamics simulations with a realistic glue potential that reproduces the hexagonal-like Au(001) reconstruction, confirm that these depressions are in fact two-dimensional $\ensuremath{\pi}/3$ dislocation dipoles originated by the relaxation of vacancy rows on the ridges of the topmost reconstructed layer. These two-dimensional dipoles are seen to dissociate into individual two-dimensional dislocations that display the characteristics of ordinary bulk dislocations, e.g. glide or climb. At higher doses $(\ensuremath{\simeq}3\ifmmode\times\else\texttimes\fi{}{10}^{14} \mathrm{ions}/{\mathrm{cm}}^{2}),$ but well below a nominal removal of 1 monolayer, vacancy islands, one atomic spacing high, are seen to nucleate on these depressions. With increasing ion damage these vacancy islands become the dominant feature. For doses of about ${10}^{15} \mathrm{ions}/{\mathrm{cm}}^{2},$ other defects related to the reconstruction, such as perpendicular reconstruction domains and unreconstructed patches of (001) square symmetry, become visible.