In comets, iron and nickel are found in refractory dust particles or in metallic and sulfide grains . So far, no iron- or nickel-bearing molecules have been observed in the gaseous coma of comets . Iron and a few other heavy atoms, such as copper and cobalt, have been observed only in two exceptional objects: the Great Comet of 1882 and, almost a century later, C/1965 S1 (Ikeya-Seki) . These sungrazing comets approached the Sun so closely that refractory materials sublimated, and their relative abundance of nickel to iron was similar to that of the Sun and meteorites . More recently, the presence of iron vapour was inferred from the properties of a faint tail in comet C/2006 P1 (McNaught) at perihelion , but neither iron nor nickel was reported in the gaseous coma of comet 67P/Churyumov-Gerasimenko by the in situ Rosetta mission . Here we report that neutral Fe I and Ni I emission lines are ubiquitous in cometary atmospheres, even far from the Sun, as revealed by high-resolution ultraviolet-optical spectra of a large sample of comets of various compositions and dynamical origins. The abundances of both species appear to be of the same order of magnitude, contrasting the typical Solar System abundance ratio.