The NA61/SHINE collaboration studies at the CERN Super Proton Synchrotron (SPS) the onset of deconfinement in hadronic matter by the measurement of particle production in collisions of nuclei with various sizes at a set of energies covering the SPS energy range. This paper presents results on inclusive double-differential spectra and mean multiplicities of $pi^{-}$ mesons produced in the 5% most textit{central} $^7$Be+$^9$Be collisions at beam momenta of 19$A$, 30$A$, 40$A$, 75$A$ and 150$A$ GeV/$c$ obtained by the so-called $h^-$ method which does not require any particle identification. The shape of the transverse mass spectra differs from the shapes measured in central Pb+Pb collisions and inelastic p+p interactions. The normalized width of the rapidity distribution decreases with increasing collision energy and is in between the results for inelastic nucleon-nucleon and central Pb+Pb collisions. The mean multiplicity of pions per wounded nucleon in textit{central} $^7$Be+$^9$Be collisions is close to that in central Pb+Pb collisions up to 75$A$GeV/$c$. However, at the top SPS energy the result is close to the one for inelastic nucleon-nucleon interactions. The results are discussed in the context of predictions for the onset of deconfinement at the CERN SPS collision energies.