Effort estimation methods are one of the important tools for project managers in controlling human resources of ongoing or future software projects. The estimations require historical project data including process and product metrics that characterize past projects. Practically, in using the estimation methods, it is a problem that the historical project data frequently contain substantial missing values. In this paper, we propose an effort estimation method based on Collaborative Filtering for solving the problem. Collaborative Filtering has been developed in information retrieval researchers, as one of the estimation techniques using defective data, i.e. data having substantial missing values. The proposed method first evaluates similarity between a target (ongoing) project and each past project, using vector based similarity computation equation. Then it predicts the effort of the target project with the weighted sum of the efforts of past similar projects. We conducted an experimental case study to evaluate the estimation performance of the proposed method. The proposed method showed better performance than the conventional regression method when the data had substantial missing values.