NGC 5128 (Centaurus A) is one of the best example to study AGN-feedback in the local Universe. At 13.5 kpc from the galaxy, optical filaments with recent star formation are lying along the radio-jet direction. We used the Atacama Pathfinder EXperiment (APEX) to map the CO(2-1) emission all along the filaments structure. Molecular gas mass of 8.2x10^7 Msun was found over the 4.2 kpc-structure which represents about 3% of the total gas mass of the NGC 5128 cold gas content. Two dusty mostly molecular structures are identified, following the optical filaments. The region corresponds to the crossing of the radio jet with the northern HI shell, coming from a past galaxy merger. One filament is located at the border of the HI shell, while the other is entirely molecular, and devoid of HI gas. The molecular mass is comparable to the HI mass in the shell, suggesting a scenario where the atomic gas was shocked and transformed in molecular clouds by the radio jet. Comparison with combined FIR Herschel and UV GALEX estimation of star formation rates in the same regions leads to depletion times of more than 10 Gyr. The filaments are thus less efficient than discs in converting molecular gas into stars. Kinetic energy injection triggered by shocks all along the jet/gas interface is a possible process that appears to be consistent with MUSE line ratio diagnostics derived in a smaller region of the northern filaments. Whether the AGN is the sole origin of this energy input and what is the dominant (mechanical vs radiative) mode for this process is however still to be investigated.