Let $G$ be a group and $\varphi \in \Aut(G)$. Then the set $G$ equipped with the binary operation $a*b=\varphi(ab^{-1})b$ gives a quandle structure on $G$, denoted by $\Alex(G, \varphi)$ and called the generalised Alexander quandle. When $G$ is additive abelian and $\varphi = -\id_G$, then $\Alex(G, \varphi)$ is the well-known Takasaki quandle. In this paper, we determine the group of automorphisms and inner automorphisms of Takasaki quandles of abelian groups with no 2-torsion, and Alexander quandles of finite abelian groups with respect to fixed-point free automorphisms. As an application, we prove that if $G\cong (\mathbb{Z}/p \mathbb{Z})^n$ and $\varphi$ is multiplication by a non-trivial unit of $\mathbb{Z}/p \mathbb{Z}$, then $\Aut\big(\Alex(G, \varphi)\big)$ acts doubly transitively on $\Alex(G, \varphi)$. This generalises a recent result of \cite{Ferman} for quandles of prime order.