Ocean acoustic tomography (OAT) is a useful tool for observing oceanographic phenomena in wide regions. For the purpose of monitoring the ocean phenomenon associated with El Niño and the Southern Oscillation (ENSO), the Central Equatorial Pacific tomography experiment was started in January 1999. The travel time perturbations due to ocean currents correspond to one to two orders of magnitude smaller than the travel time signals due to sound-speed perturbations. In the conventional method, the travel time difference by the ocean current is measured using amplitude information of the received signal. Because of the attenuation of long-range propagation, it is difficult to measure the travel time difference precisely. We present the estimation results of the travel time difference in reciprocal transmission data using the phase difference between reciprocal transmissions. Since the wave front is very stable in space and time, the vertical arriving angle of ray can be measured using the phase differences between the receivers of a 30-m-long receiving array. From the ray identification results, the travel time difference between corresponding rays of reciprocal transmissions can be estimated. Since the phase of a ray signal is very stable, the precision of the travel time difference using phase difference is 6 times (±0.08 ms) higher than the conventional estimation. The travel time differences, using this method, have reasonable magnitudes, and then the low-frequency trend is presumably caused by mesoscale fluctuations in this ocean region.