The plan was to display the flag for five months, but now it is being removed after only 19 days. The art gallery claims that it is due to escalating tensions and security risks - and it is not the first time.
Thirty years ago, the same piece was taken down from another gallery, following similar protests.
In New Zealand, desecrating the national flag is illegal and local police tell AP that they are investigating several complaints related to the flag artwork.
The artwork was created in 1995 by Diane Prince, as a response to a government policy that limited compensation to the country's indigenous people for land seizures that occurred during Britain's colonization in the 19th century.
The artwork - and the protests against it - have revived long-standing debates in the country about artistic expression, national symbols, and its colonial history.