Formation of defects in hexagonal boron nitride (h-BN) under low-energy argon or nitrogen ion bombardment has been studied by near-edge X-ray absorption fine structure (NEXAFS) around boron and nitrogen K-edges and X-ray photoemission spectroscopy (XPS) from B1s and N1s core levels. Breaking of B–N bonds and formation of nitrogen vacancies have been identified in the B K-edge NEXAFS and B1s XPS measurements, followed by the formation of molecular nitrogen, N 2, at interstitial positions for both argon and nitrogen bombardments. The formation of N 2 produces a sharp resonance in the low-resolution NEXAFS spectra around the N K-edge, showing characteristic vibrational fine structure in high-resolution measurements.