The surface concentrations of copper and iron in currently used silicon wafers are lower than 1014 atoms·m–2. To determine such ultra-trace elements accurately by neutron activation analysis, we measured the efficiencies of a well-type Ge detector for59Fe -rays and64Cu annihilation -rays. We also developed methods for preparing samples for copper and iron analysis including a low-temperature silicon direct-bonding technique. We have applied these techniques to determine copper and iron on the surface of clean silicon wafers, and obtained concentrations of 1013–1014 atoms·m–2.