Context : The formation processes and the evolutionary stages of high-mass stars are poorly understood compared to low-mass stars . Large-scale surveys are needed to provide an unbiased census of high column density sites which can potentially host precursors to high-mass stars . Aims : The ATLASGAL survey covers 420 sq . degree of the Galactic plane , between -80 ^ { \circ } < \ell < +60 ^ { \circ } at 870 \umu m. Here we identify the population of embedded sources throughout the inner Galaxy . With this catalog we first investigate the general statistical properties of dust condensations in terms of their observed parameters , such as flux density and angular size . Then using mid-IR surveys we aim to investigate their star-formation activity and the Galactic distribution of star-forming and quiescent clumps . Our ultimate goal is to determine the statistical properties of quiescent and star-forming clumps within the Galaxy and to constrain the star-formation processes . Methods : We optimized the source extraction method , referred to as MRE-GCL , for the ATLASGAL maps in order to generate a catalog of compact sources . This technique is based on a multi-scale filtering to remove extended emission from clouds to better determine the parameters corresponding to the embedded compact sources . In a second step we extract the sources by fitting 2D Gaussians with the Gaussclumps algorithm . Results : We have identified in total 10861 compact sub-millimeter sources with fluxes above 5 \sigma . Completeness tests show that this catalogue is 97 % complete above 5 \sigma and > 99 % complete above 7 \sigma . Correlating this sample of clumps with mid-infrared point source catalogues ( MSX at 21.3 \umu m and WISE at 22 \umu m ) we have determined a lower limit of 33 % that are associated with embedded protostellar objects . We note that the proportion of clumps associated with mid-infrared sources increases with increasing flux density , achieving a rather constant fraction of \sim 75 % of all clumps with fluxes over 5 Jy/beam being associated with star-formation . Examining the source counts as a function of Galactic longitude we are able to identify the most prominent star forming regions in the Galaxy . Conclusions : We present here the compact source catalog of the full ATLASGAL survey and investigate their characteristic properties . From the fraction of the likely massive quiescent clumps ( \sim 25 % ) we estimate a formation time-scale of \sim 7.5 \pm 2.5 \times 10 ^ { 4 } yr for the deeply embedded phase before the emergence of luminous YSOs . Such a short duration for the formation of high-mass stars in massive clumps clearly proves that the earliest phases have to be dynamic with supersonic motions .