The scientific team on the expedition also included the artist Selleny, the zoologists Frauenfeld and Zelebor, and the botanists Schwarz and Jelinek. All were under the direction of the chief scientist Karl von Scherzer, who later published a three-volume account of the expedition in his role as historiographer.
Hochstetter was asked to complete a full investigation of recently discovered coal deposits in the Drury and Hunua districts south of Auckland. On completing his report he was invited to stay on to complete further geological research in New Zealand.
After the Novara expedition left Auckland on 8 January 1859 to sail on to Tahiti, Hochstetter worked for the Auckland Provincial Government. He completed a detailed survey of the Auckland isthmus area with its numerous volcanic cones and other points of eruption and prepared the first geological map of the area, which was later published in Germany.
Hochstetter then left on a major expedition to survey and explore the southern parts of the Province of Auckland, going as far south as Lake Taupo and from there north towards the hot lakes district and Mt Tarawera and from Tauranga back to Auckland.
On completion of his task in Auckland he gave a public lecture on the geology of Auckland before heading south at the invitation of the Nelson Provincial Government to explore the area around Nelson. He left New Zealand on 2 October 1859 and travelled back to Vienna via Australia.