A new three-dimensional GPS ionospheric tomography technique is developed that uses total electron content (TEC) data from the dense Global Position System (GPS) receiver network, GPS Earth Observation Network (GEONET) in Japan, and it will not require an ionospheric model as the initial guess that will bias the reconstruction of electron density. The GEONET is operated by Geospatial Information Authority of Japan and consists of more than 1200 receivers; this high density and wide coverage helps to reconstruct the electron density distribution in the ionosphere with high spatial resolution. This tomography technique uses a constrained least squares fit to reconstruct the three-dimensional electron density distributions. This method is different to most other techniques as they require a background ionospheric model as an initial guess that could bias the reconstructed electron density. It rather uses a prior condition that the electron density should not exceed a certain value that is determined by the restrain parameter, which is derived from the NeQuick model. Its independency of the initial guess from a model will make it useful even in disturbed conditions. This paper presents results that are obtained by using this new tomographic technique. The reconstruction of three-dimensional ionospheric tomograms is demonstrated using the GPS data, and the reliability and robustness are checked with simulated tomograms obtained using the synthetic GPS-TEC data produced using NeQuick model.