This paper is part of the series presenting the final results obtained by the ESO Imaging Survey (EIS) project. It presents new J and Ks data obtained from observations conducted at the ESO 3.5m New Technology Telescope (NTT) using the SOFI camera. These data were taken as part of the Deep Public Survey (DPS) carried out by the ESO Imaging Survey program, significantly extending the earlier optical/infrared EIS-DEEP survey presented in a previous paper of this series. The DPS-IR survey comprises two observing strategies: shallow Ks observations providing nearly full coverage of pointings with complementary multi-band (in general UBVRI) optical data obtained using ESO's wide-field imager (WFI) and deeper J and Ks observations of the central parts of these fields. Currently, the DPS-IR survey provides a coverage of roughly 2.1 square degrees (~300 SOFI pointings) in Ks with 0.63 square degrees to fainter magnitudes and also covered in J, over three independent regions of the sky. The goal of the present paper is to briefly describe the observations, the data reduction procedures, and to present the final survey products which include fully calibrated pixel-maps and catalogs extracted from them. The astrometric solution with an estimated accuracy of <0.15" is based on the USNO catalog and limited only by the accuracy of the reference catalog. The final stacked images presented here number 89 and 272, in J and Ks, respectively, the latter reflecting the larger surveyed area. The J and Ks images were taken with a median seeing of 0.7" and 0.8". The images reach a median 5 sigma limiting magnitude of J_AB~23.06 as measured within an aperture of 2", while the corresponding limiting magnitude in Ks_AB is ~21.41 and ~22.16mag for the shallow and deep strategies. Although some spatial variation due to varying observing conditions is observed, overall the observed limiting magnitudes are consistent with those originally proposed. The quality of the data has been assessed by comparing the measured magnitude of sources at the bright end directly with those reported by the 2MASS survey and at the faint end by comparing the counts of galaxies and stars with those of other surveys to comparable depth and to model predictions. The final science-grade catalogs together with the astrometrically and photometrically calibrated co-added images are available at CDS.