Rossi X-ray Timing Explorer (RXTE) observations of the X-ray transient pulsar 2S 1417-62 between 1999 November and 2000 August with a total exposure of similar to394 ks have been analysed. Observations include a main outburst followed by a series of mini outbursts. Changes in pulse morphology and pulse fraction were found to be related to the changes in X-ray flux. Particularly low X-ray flux regions were found to have significantly lower pulse fractions with different pulse morphologies. The 3-60 keV Proportional Counter Array (PCA) High-Energy X-ray Timing Experiment (HEXTE) main outburst spectrum was modelled with an absorbed power-law model with high-energy cut-off and a Gaussian iron line complex feature. Using the same spectral model, individual 3-20 keV PCA spectra were found to be softer and less absorbed in low X-ray flux regions between outbursts. Spectral studies showed that hydrogen column density was correlated, and the power-law index was anticorrelated with the 3-20 keV X-ray flux. X-ray flux related spectral and timing features in 2S 1417 62, except for low X-ray flux regions, were interpreted as a sign of disc accretion with a similar accretion geometry with a varying mass accretion rate ((M)over dot), whereas spectral and timing features of the low X-ray flux regions were interpreted as a sign of possible temporary accretion geometry change prior to the next periastron where (M)over dot increases again to restore the original accretion geometry.