Context. Active galactic nuclei (AGNs) are very luminous galaxies from the ultraviolet (UV) to the far infrared (FIR). To study regions near the core, which are dominated by dust, IR is the perfect spectral range because of the lower optical depth of the dust. However, these galaxies are usually distant, and the structures near the core are faint compared to the central source. High resolution and high contrast are mandatory to study the inner structures of AGNs and better understand the interaction between the central core and its surroundings. Aims. Our goal is to propose an explanation for the coronal lines in our spectra of NGC 1068 at a far distance (few tens of parsec) from the central source inside wave-like structures that we call nodules. Methods. NGC 1068 was observed with NaCo at ESO/VLT, using long-slit spectroscopy at 2.2 μm and 3.5 μm. Reduced spectra were compared to the output of Cloudy, using various ionizing continua: the continuum of the central source, young stars, and radiative shocks caused by the jet. Results. For the first time, thanks to the resolution provided by NaCo, near-IR coronal emission can be precisely associated to structures observable in the IR broad-band images. We found that coronal lines observed in the nodules cannot be caused by photoionization by the central source but are instead caused by a local jet-induced ionizing continuum. In addition, studying the Brackett-γ line (Brγ) and CO 2-0 band head, we deduced a star density within the four nodules (∼800 000 stars) compatible with super star cluster (hereafter SSC) models.