VanKoughnet efficiently reorganised the department of Agriculture, and in particular took effective measures to check the ravages of the Hessian fly and weevil. In August 1858, he was named Commissioner of Crown Lands in the Cartier-Macdonald administration, and held office for four years. In 1860, he was also appointed the first Chief Superintendent of Indian Affairs. During his time as Commissioner of Crown Lands he established the system of selling townships en bloc, and opened up some of the best colonization roads.