Using GAP one finds that there are $589$ nonabelian groups of order $2187$ whose automorphism group is abelian. All the automorphism groups are isomorphic to $C_3^{12}$. The list of those groups is $\operatorname{SmallGroup}(2187,n)$ for
6172~6183, 6187~6189, 6191, 6195, 6221~6229, 6233~6235, 6269~6304, 6314~6352,
6356~6363, 6365~6366, 6368~6376, 6378~6383, 6385, 6387~6391, 6393~6396, 6399,
6567~6575, 6589, 6593~6604, 6606, 6612~6614, 6616~6624, 6630~6632, 6634~6642,
6644~6647, 6649~6651, 6653~6655, 6657, 6660, 6663, 6666~6667, 6674~6676, 6679,
6683~6686, 6688~6709, 6712, 6714, 6717~6718, 6722, 6725, 6728~6732, 6734, 6736,
6738, 6740~6751, 6753~6762, 6764, 6767~6771, 6773~6775, 6777, 6779~6782, 6788~6790,
6792~6793, 6795~6797, 6801~6802, 6804, 6808~6818, 6823~6831, 6836~6844, 6846~6853,
6855~6864, 6866~6872, 6874~6887, 6889~6910, 6913~6914, 6916, 6919~6922, 6924,
6926~6935, 6937~6940, 6942~6977, 6979~6981, 6983, 6985~6988, 6990, 6992~6998,
7001, 7003~7024, 7026~7028, 7030~7032, 7034~7047, 7049~7058, 7060, 7062~7068,
7070, 7072~7079, 7081, 7083~7085, 7087~7092, 7094~7097, 7101~7111, 7122, 7164,
7166, 7168~7177, 7179, 7181, 7183~7192, 7194, 7196, 7198~7207.
Also, there are no nonabelian groups of order $729$ or $15625$ with abelian automorphism group.
Edit: The GAP code is
list_aut_abelian := function(n)
local m, i, G;
m := NumberSmallGroups(n);
for i in [1..m] do
G := SmallGroup(n,i);
if not IsAbelian(G) then
G := AutomorphismGroup(G);
if IsAbelian(G) then Print("Aut(SmallGroup(", n, ",", i, ") = ",
StructureDescription(G), "\n"); fi;
fi; od; end;