A properly determined separation minima applied in Air Traffic Management(ATM) is critical for safe and efficient aircraft operations. The separation minima is primarily determined by the accuracy performance of surveillance system, and, due to the stringent aviation safety standard, the position accuracy of the surveillance system must be estimated with a high level of reliability. This study proposed a method for estimating the position accuracy of surveillance system with a relatively small amount of data by finding upper confidence limit instead of maximum likelihood values of unknown parameters. Through the proposed method, it is possible to determine a required separation minima with a more reliability in the face of data scarcity which often occurs when we implement a new surveillance system such as Automatic Dependent Surveillance-Broadcast (ADS-B).