An improved procedure is proposed to determine the accurate values of deep level parameters in Schottky diodes with non-negligible majority-carrier capture rate due to a leakage current. Numerical modeling of deep level transient spectroscopy signals from the EL2 center in GaAs demonstrates the degree to which leakage currents of various magnitudes can distort the spectra and without correction lead to misleading deep level parameters. Finally, deep levels in n-type InP Schottky diodes have been examined using a commercially available lock-in spectrometer DLS-82E to demonstrate the practical application of the proposed procedure.