MacGregor's experience with native races led to his being appointed administrator of British New Guinea in 1888. Here he had to deal with a warlike people separated in many tribes, and his great problem was to get them to live together in reasonable amity. It was necessary at times to make punitive expeditions, but bloodshed was avoided as much as possible, and by tact and perseverance MacGregor eventually brought about a state of law and order. He did a large amount of exploration not only along the coast but into the interior. Andrew Gibb Maitland was seconded as geologist in 1891. In 1892 the position was sufficiently settled to enable him to publish a "Handbook of Information for intending Settlers in British New Guinea". He was awarded the 1896 Founder's Medal of the Royal Geographical Society for his services to geography.