X-ray absorption spectroscopy of epitaxial GeMn thin films reveals an experimentally indistinguishable electronic configuration of Mn atoms incorporated in Ge(1-x)Mn(x) nanoclusters and in precipitates of the intermetallic compound Mn(5)Ge(3), respectively. However, the average magnetic response of thin films containing Ge(1-x)Mn(x) nanoclusters is lower than the response of films containing Mn(5)Ge(3) precipitates. This reduced magnetic response of Ge(1-x)Mn(x) nanoclusters is explained in terms of a fraction of Mn atoms being magnetically inactive due to antiferromagnetic coupling or the presence of structural disorder. A determination of the role of magnetically inactive Mn atoms in the self-assembly of the thermodynamically metastable Ge(1-x)Mn(x) nanoclusters seems to be an essential ingredient for an enhanced control of this promising high Curie temperature magnetic semiconductor.