We investigated electrical conduction of anatase Ti0.94Nb0.06O2 (TNO) epitaxial thin films in relation to oxygen defects generated by post-annealing. Annealing of TNO in oxygen was found to cause dramatic decreases in ne. Resonant photoemission spectroscopy measurements revealed that a deep acceptor state just above the top of valence band evolves, synchronized with the decrease of ne. We proposed that the acceptor state originates from interstitial oxygen atoms combined with Nb dopants and compensates electron carriers.