This paper presents the direct relationship between the positioning accuracy of linear magnetic encoders and the surface flaws on their measuring scales. Measuring scales having recording media composed of electrodeposited Co-rich coatings are imprinted to form mimic surface flaws of particulate or stripe shapes. Effects of flaw sizes and stripe directions on the encoder positioning accuracy have been investigated. Benchmarked with an un-flawed scale which has an accuracy error of ± 2.0 μm in a 6.0 cm length, the flawed scales with a flaw width > 130 μm and a flaw depth > 4 ∼ 5 μm present accuracy variation in the 2-centimeter flaws regions on the measuring scales. Compared with particulate flaws, stripe flaws are more detrimental, especially the stripes being perpendicular (i.e., 90°) to the moving direction of read head. Accuracy variation behaviors due to surface flaws of electrodeposited measuring scales have been unambiguously demonstrated for long-length high-accuracy magnetic encoders.