Software effort estimation is a critical task for successful software development, which is necessary for appropriately managing software task assignment and schedule and consequently producing high-quality software. Function point (FP) metrics are commonly used for software effort estimation. To build a good effort estimation model, independent explanatory variables corresponding to FP metrics are required to avoid a multicollinearity problem. For this reason, previous studies have tackled analyzing correlation relationships between FP metrics. However, previous results on the relationships have some inconsistencies. To obtain evidence for such inconsistent results and achieve more effective effort estimation, we propose a novel analysis, which investigates causal-effect relationships between FP metrics and effort. We use an advanced linear non-Gaussian acyclic model called BayesLiNGAM for our causal-effect analysis, and compare the correlation relationships with the causal-effect relationships between FP metrics. In this paper, we report several new findings including the most effective FP metric for effort estimation investigated by our analysis using two datasets.