Naval weapons systems of the Republic of Korea are acquired through the Defense Planning Management System. Recently, acquisition of some naval ships have been delayed, and the causes of the delays have been recognized as inappropriate project management at the Execution Phase. However, we argue that the delay problem in naval ships acquisition should be approached, with due regard for the entire Defense Planning Management System. That is, We should try to investigate from Planning Phase to those of Programming, Budgeting and Execution Phases. Therefore, in this study, we investigated the actual cases of the delay in naval acquisition at all phases of the Defense Planning Management System. Based on the investigation, we tried to identify the naval ship Acquisition Delay Factors and find out the Weights of those factors. As the next step, we calculated the Influence Measures on the naval missions, including the Cost of Naval Capability Gap derived from the delays in acquisition of naval ships. As a final step, we calculated the Acquisition Delay Measures based on the interrelationship between the Acquisition Delay Factors and the Influence Measures. Then we evaluated and analyzed what the results stand for. Finally, we made suggestions for future improvement. The improvement suggestions we made for preventing delay in acquisition of naval ships in this study are as follows. First, we need a shift in perception. It is necessary to measure the Acquisition Delay Factors in acquiring naval ships and manage them from the Planning Phase. Second, resolution must be concerted efforts. All relevant agencies, not just a few, should work together to resolve the problems of acquisition delay. Third, analysis must be based on the accumulation of data. This allows the elaborating of naval ship Acquisition Delay Factors and Delay Measures. If this research method is applied to other military weapons systems in the future, we may be able to not just identify the Acquisition Delay Factors in acquisition of other military weapons systems, but also pursue improvement in those cases.