Low-mass compact galaxies (ultracompact dwarfs -UCDs-and compact ellipticals -cEs-) populate the stellar size-mass plane between globular clusters and early-type galaxies. Known to be formed either in-situ with an intrinsically low mass or resulting from the stripping of a more massive galaxy, the presence of a supermassive or an intermediate-mass black hole (BH) could help discriminate between these possible scenarios. With this aim, we have performed a multiwavelength search of active BH activity, i.e. active galactic nuclei (AGN), in a sample of 937 low-mass compact galaxies (580 UCDs and 357 cEs). This constitutes the largest study of AGN activity in these types of galaxies. Based on their X-ray luminosity, radio luminosity and morphology, and/or optical emission line diagnostic diagrams, we find a total of 11 cEs that host an AGN. We also study for the first time the location of both low-mass compact galaxies (UCDs and cEs) and dwarf galaxies hosting AGN on the BH-galaxy scaling relations, finding that low-mass compact galaxies tend to be overmassive in the BH mass-stellar mass plane but not as much in the BH mass-stellar velocity dispersion correlation. This, together with available BH mass measurements for some of the low-mass compact galaxies, supports a stripping origin for the majority of these objects that would contribute to the scatter seen at the low-mass end of the BH-galaxy scaling relations. However, the differences are too large to be explained solely by this scatter, and thus our results suggest that a flattening at such low-masses is also plausible, happening at a velocity dispersion of ∼20-40 km s−1.