dˈʊɹɹɪŋ ðə wˈʌn θˈaʊzənd ˈeɪthˈʌndɹɪd sˈɪksti z, dʒˈoʊnz ˈɪntɹɛsts ɐɡˈɛn tˈɜːnd tə ʃˈɪpɪŋ, fˈɜːstli æz ɐ ʃˈɛɹhoʊldɚɹ ʌvðə ʃˈɔːɹtlˈɪvd ɑːtˈeɪɡoʊ stˈiːm ʃˈɪp kˈʌmpəni, ænd ðˈɛn θɹuː hɪz ˈoʊn vˈɛntʃɚ, ðə hˈɑːɹbɚ stˈiːm nˌævɪɡˈeɪʃən kˈʌmpəni, wˌɪtʃ sˈɜːvd ðə pˈoːɹts ʌv dˈʌnɪdˌɪn, pˈoːɹt tʃˈælmɚz, ænd ˈoʊmɑːɹɹˌuː, ænd lˈeɪɾɚɹ ˈɔːlsoʊ tɹˈeɪdᵻd wɪð hˈɑːkɪtˌɪkə ɔnðə wˈɛst kˈoʊst.
During the 1860s, Jones' interests again turned to shipping, firstly as a shareholder of the short-lived Otago Steam Ship Company, and then through his own venture, the Harbour Steam Navigation Company, which served the ports of Dunedin, Port Chalmers, and Oamaru, and later also traded with Hokitika on the West Coast.