We characterize low-loss electron-beam evaporated niobium thin films deposited under ultra-high vacuum conditions. Slow deposition yields films with a high superconducting transition temperature ($9.20 pm 0.06 rm ~K$) as well as a residual resistivity ratio of $4.8$. We fabricate the films into coplanar waveguide resonators to extract the intrinsic loss due to the presence of two-level-system fluctuators using microwave measurements. For a coplanar waveguide resonator gap of $2~mu rm m$, the films exhibit filling-factor-adjusted two-level-system loss tangents as low as $1.5 times 10^{-7}$ with single-photon regime internal quality factors in excess of one million after removing native surface oxides of the niobium.