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The homes, in Bradshaw St, had been vacant for some time, but the increasingly dangerous structures had been used by transients.
It is understood the owner of the properties - who did not wish to comment - decided to demolish the houses as they were unsafe for use.
Demolition work began Monday and was continuing on Tuesday morning, until the intervention of Heritage New Zealand.
The houses date from before 1900, and by law were defined as archaeological sites.
The Heritage New Zealand Pouhere Taonga Act says unless authority is granted, no-one can modify or destroy any part of a site if that person knows, or ought reasonably to have suspected, that the site is an archaeological site.
The owners are now working with Heritage New Zealand to apply for authority for demolition to continue.