The paramagnetic spin-triplet superconductor UTe$_2$ has attracted significant attention because of its exotic superconducting properties including an extremely high upper critical field and possible chiral superconducting states. Recently, ultraclean single crystals of UTe$_2$ have become available, and thus measurements on these crystals are crucial to elucidate the intrinsic superconducting properties. Here, we report the thermodynamic critical field $H_{\rm c}$, the lower critical field $H_{\rm c1}$, and the upper critical field $H_{\rm c2}$ at low fields of these high-quality single crystals. From the comparison of the anisotropies in $H_{\rm c1}$ and $H_{\rm c2}$, we find that the experimental $H_{\rm c1}$ values with the magnetic field along $b$- and $c$-axes are anomalously enhanced, showing unusual low-temperature upturns. We propose an effect of the strong Ising-like ferromagnetic fluctuations on the vortex line energy as the origin of the anisotropic enhancement of $H_{\rm c1}$.