The area of indigenous vegetation and habitat remaining on New Zealand's primary agricultural lands continues to decrease, but it has been difficult to obtain reliable estimates of the extent and causes of loss. We assess change and identify predictors of vegetation clearance in 856 recommended areas for protection (RAPs) from 35 ecological districts in the North and South Islands, New Zealand, for the period 1989 to 2015. Over 27 years, 7152 ha of these RAPs were cleared (2.3% by area), with rates varying over space and time. Native forest was least commonly cleared (422 ha removed), followed by native non-woody vegetation (1294 ha), native shrubland (1378 ha), and 'other' vegetation (4058 ha). The probability of clearance peaked during 2001 to 2008 at 0.14% yr-1 , but it was still nearly double the 1989-2001 levels (0.06% yr-1) from 2008 to 2015 (0.11% yr-1). The annualised clearance probabilities after 2001 were comparable to the rates of deforestation in the pre-1840 period of human settlement and about a third of that recorded from 1840 to 1970, the most intensive known period of anthropogenic clearance in New Zealand. Clearance rates were higher around the edges of small RAPs without legal protection and in drier, cooler areas, generally and increasingly over time. Amount of surrounding cropping/horticulture was negatively associated with clearance, as initially was dairy before developing a slightly positive association. Forestry was positively associated with clearance up until 2008. Our results show proportionally greater clearance of marginal agricultural land with high biodiversity values as time goes on, probably facilitated by the increasing use of technology, such as irrigation and fertilisation, to circumvent environmental limitations to plant growth. These results demonstrate ongoing attrition of the highest-value native habitat remaining on private land, and the inadequacy of the current protection framework to safeguard it.