This study is aimed at developing an eddy-current-based SQUID-NDE system for in-situ inspection of micro flaws on thin copper heat exchanger tubes. The system employs a high temperature superconductor (HTS-) SQUID gradiometer and a Helmholtz-coil-type inducer. As specimens, copper tubes 6.35 mm in outer diameter and 0.8 mm in thickness with artificial surface flaws of several tens μm in depth were inspected using the system. Magnetic response due to a flaw of 10 μm in depth on the tube moving at 32 m/min was successfully detected while applying an excitation field of 10 μT at 3 kHz to the tube. Numerical simulations were also conducted to evaluate how many sensors would be required for inspection around the circumference of an entire tube.