We study N=6 gauged supergravity in three dimensions with scalar manifolds $\frac{SU(4,k)}{S(U(4)\times U(k))}$ for $k=1,2,3,4$ in great details. We classify some admissible non-compact gauge groups which can be consistently gauged and preserve all supersymmetries. We give the explicit form of the embedding tensors for these gauge groups as well as study their scalar potentials on the full scalar manifold for each value of $k=1,2,3,4$ along with the corresponding vacua. Furthermore, the potentials for the compact gauge groups, $SO(p)\times SO(6-p)\times SU(k)\times U(1)$ for $p=3,4,5,6$, identified previously in the literature are partially studied on a submanifold of the full scalar manifold. This submanifold is invariant under a certain subgroup of the corresponding gauge group. We find a number of supersymmetric AdS vacua in the case of compact gauge groups. We then consider holographic RG flow solutions in the compact gauge groups $SO(6)\times SU(4)\times U(1)$ and $SO(4)\times SO(2)\times SU(4)\times U(1)$ for the k=4 case. The solutions involving one active scalar can be found analytically and describe operator flows driven by a relevant operator of dimension 3/2. For non-compact gauge groups, we find all types of vacua namely AdS, Minkowski and dS, but there is no possibility of RG flows in the AdS/CFT sense for all gauge groups considered here.