This invention provides a system and method for generating camera calibrations for a vision system camera along three discrete planes in a 3D volume space that uses at least two (e.g. parallel) object planes at different known heights. For any third (e.g. parallel) plane of a specified height, the system and method then automatically generates calibration data for the camera by interpolating/extrapolating from the first two calibrations. This alleviates the need to set the calibration object at more than two heights, speeding the calibration process and simplifying the user's calibration setup, and also allowing interpolation/extrapolation to heights that are space-constrained, and not readily accessible by a calibration object. The calibration plate can be calibrated at each height using a full 2D hand-eye calibration, or using a hand-eye calibration at the first height and then at a second height with translation to a known position along the height (e.g. Z) direction.