Accuracy of implant position reproduction according to various types of scanners, implant placement depths, and tooth positions are unknown. The purpose of this study was to compare the accuracy of implant position reproduction for differences in the exposed length of the implant scan body according to scanner type and tooth position. Implants were placed at the positions of the lateral incisor, first premolar, and first molar in the study model at the bone level and submerged 1.5 mm, 3.0 mm, 4.5 mm, and 6.0 mm. The completed models were scanned with one type of tabletop scanner and three types of intraoral scanners (TRIOS 3, i500, and CS3600). A matching process was performed for all scan data to superimpose abutment library data on the scan body, and the root mean square errors were analyzed in three dimensions to evaluate the position reproducibility of the replaced abutment library. In the trueness analysis, the error increased rapidly for an implant placement depth of 4.5 mm, and was largest for a submersion of 6.0 mm. The precision analysis confirmed that the error increased for depths of at least 3.0 mm. The analysis by position identified that the accuracy was lowest for an implant placed at the position of the lateral incisor. These findings indicate that special care is required when making an impression of a deep implant with an optical scanner.