We investigate the interstellar medium (ISM) towards seven TeV gamma-ray sources thought to be pulsar wind nebulae (PWNe) using Mopra molecular line observations at 7mm [CS(1-0), SiO(1-0,v=0)], Nanten CO(1-0) data and the SGPS/GASS Hi survey. We have discovered several dense molecular clouds co-located to these TeV gamma-ray sources, which allows us to search for cosmic-rays (CRs) coming from progenitor SNRs or, potentially, from PWNe. We notably found SiO(1-0,v=0) emission towards HESS J1809−193, highlighting possible interaction between the adjacent supernova remnant SNR G011.0−0.0 and the molecular cloud at d ∼ 3.7 kpc. Using morphological features, and comparative studies of our column densities with those obtained from X-ray measurements, we claim a distance d ∼ 8.6 − 9.7 kpc for SNR G292.2−00.5, d ∼ 3.5 − 5.6 kpc for PSR J1418−6058 and d ∼ 1.5 kpc for the new SNR candidate found towards HESS J1303−631. From our mass and density estimates of selected molecular clouds, we discuss signatures of hadronic/leptonic components from PWNe and their progenitor SNRs. Interestingly, the molecular gas, which overlaps HESS J1026−582 at d ∼5 kpc, may support a hadronic origin. We find however that this scenario requires an undetected cosmic-ray accelerator to be located at d < 10 pc from the molecular cloud. For HESS J1809−193, the cosmic-rays which have escaped SNR G011.0−0.0 could contribute to the TeV gamma-ray emission. Finally, from the hypothesis that at most 20% the pulsar spin down power could be converted into CRs, we find that, among the studied PWNe, only those from PSR J1809−1917 could potentially contribute to the TeV emission.