Estimating underwater target state variables(position, velocity, course, etc) is necessary to counteract threatening targets. In passive sonar systems, conventional target motion analysis(TMA) techniques using bearing and frequency measurements of an underwater target are widely introduced. However, it is not clear how conventional TMA techniques can be used if some of frequency measurements are unavailable during parts of the scenario, partially unavailable frequency measurements are common in the ocean with complicated acoustic conditions where frequency measurements often come and go. This paper proposes a new TMA algorithm, which is robust to partially unavailable frequency measurements, using the frequency measurements fusion method.