A probe position error detecting method and apparatus in a probe-based data storage system are provided. The method includes preparing servo codes, which are Gray codes. The Gray codes have a Hamming distance of 1 and satisfy alternate conditions for Q (a natural number) and Q+1, the conditions being based on the numbers of “1” bits of codewords of the Gray codes. The method further includes detecting a probe position error from a signal read by a servo probe when the servo probe consecutively scans “1” bits of codewords of the servo codes when tracking. The apparatus includes: a plurality of servo probes; a tracking condition checker; a plurality of position error detectors that correspond to the plurality of servo probes, respectively; and an average position error calculator. Probe position errors are be detected with a stable noise characteristic using fewer probes.