The Low Energy High Intensity Proton Accelerator (LEHIPA) has been commissioned to the design energy of 20 MeV at BARC, India. The low energy beam transport (LEBT) channel of LEHIPA consists of two solenoids and drift spaces for matching the 50 keV proton beam from the ECR ion source (ECR-IS) to the RFQ. The ion beam extracted from the ECR-IS also contains molecular species like H2+ and H3+. Proton fraction in the beam is found to degrade slowly with time due to surface contamination of the plasma chamber and this reduction in proton beam current has implications for longitudinal and transverse beam dynamics. Hence, it becomes important to characterise the beam at different proton fraction levels to understand the end-to-end beam dynamics of LEHIPA. Computed Tomography (CT) technique has been used for the beam phase-space reconstruction in LEHIPA, using a Python program, incorporating the feature of filtering secondary species from the beam profiles measured using slit scanners in the LEBT. Simultaneous Algebraic Reconstruction Technique (SART) is used in the reconstruction since it is identified to be a better technique for a limited number of projections. The reconstruction program is benchmarked with the TraceWin beam dynamics code and implemented on the measured beam profiles to recreate the phase space distribution at the beginning of LEBT. Further, the tomographic reconstruction method is compared with the solenoid scan method and the rms emittance values are found to be in good agreement. The measured tomographic phase space distribution has then been used as TraceWin input for LEHIPA end-end beam dynamics simulations and the LEHIPA beam line parameters are re-optimized for minimum beam emittance growth. This paper presents the simulations of CT technique, benchmarking simulations with TraceWin, phase space reconstruction with measured beam profiles and beam dynamics studies of LEHIPA using the reconstructed beam distributions.