In InGaN-based LEDs, an InGaN layer underlying active region has been widely used to improve the luminescence efficiency of the quantum wells (QWs). It has been reported recently that the role of InGaN underlayer (UL) is to block the diffusion of point defects or surface defects in n-GaN into QWs. The type and the source of the point defects need further investigations. In this paper, using temperature-dependent photoluminescence (PL) measurements, we observe emission peak related to nitrogen vacancies (VN) in n-GaN. In combination with secondary ion mass spectroscopy (SIMS) measurement and theoretical calculation, it is found that VN concentration in n-GaN is as high as about 3 × 1018 cm-3 in n-GaN grown with low growth V/III ratio and can be suppressed to about 1.5 × 1016 cm-3 by increasing growth V/III ratio. Luminescence efficiency of QWs grown on n-GaN under high V/III ratio is greatly improved. These results indicate high density of nitrogen vacancies are formed in n-GaN layer grown under low V/III ratio and diffuse into quantum wells during epitaxial growth and reduce the luminescence efficiency of the QWs.