Dartist,
From the quoted text below, I would say that "Native refers to First Nation individuals.
Instructions on how the census information was to be collected was not included in the census acts. Thus the following information is taken from the schedules themselves and from the sources footnoted at the end of the document. All statistics are taken from the appendix, "Population Returns and other Statistics of the Province of New Brunswick," pages iii to xxxviii.
...
Based upon the final report of the census, "Race" indicated whether the person was 'White', 'Coloured', or 'Indian'. The population of New Brunswick was made up of 191,626 'Whites', 1,058 'Coloureds' and 1,116 'Indians'.
Cheers,