In 1789, Hunter, after leave in England, was appointed acting Superintendent of British Honduras in 1790, following the suspension of incumbent Edward Despard. He held that position until 1791 and was said to have administered the new colony in an authoritarian manner. He returned to England in 1793 and was given the rank of colonel serving in Europe and then the Caribbean before becoming a military governor in County Wexford, Ireland following the Irish Rebellion of 1798.
Hunter died unexpectedly in 1805 in Quebec and was buried at Cimetière Anglican Saint-Matthew. Alexander Grant became administrator of Upper Canada and continued Hunter's policies until a new lieutenant governor, Francis Gore, arrived from Britain in August 1806.
Hunterstown, a geographic township and village in the Municipality of Saint-Paulin, Quebec, was named after him.[1]