Several bright emission line regions are observed in the central 100 parsecs of the active galaxy NGC 1068. We aim to determine the properties and ionization mechanism of three regions: the nucleus itself (B), and two clouds located 0.3" and 0.7" North of it (C and D). We have combined SPHERE (0.95-1.65um) and SINFONI (1.5-2.45um) spectra for the three regions B, C and D. We compare these spectra to several CLOUDY photoionization models and to the MAPPINGS III Library of Fast Radiative Shock Models. The emission line spectra of the three regions are almost identical to each other, and contribute to most of the emission line flux in the nuclear region. The emitting media contain multiple phases, the most luminous of which have temperatures ranging from 104.8K to 106K. Central photoionization models can reproduce some features of the spectra, but the fast radiative shock model provides the best fit to the data. The similarity between the three regions indicates that they belong to the same class of objects. Based on our comparisons, we conclude that they are shock regions located where the AGN jet impacts massive molecular clouds.