The message, which incited violence against the Indian community, was first spotted on Saturday near Papatoetoe Central School.
Another piece of graffiti with the same message was found inside a public toilet in Royal Oak.
The 61-year-old has been charged with offensive behaviour and wilful damage.
Counties Manukau West Area Commander Inspector Dave Christoffersen said a local man was arrested on Thursday, and was due in Manukau District Court later in the day.
"Given the threatening nature of the graffiti, our team has been making enquiries throughout the week which has led to a quick arrest," he said.
Inspector Christoffersen said police were aware the incident had caused concern for communities.
"I can reassure the community that we have assessed this particular event as an isolated incident and that there is no wider risk to the community.
"We have made this assessment with information obtained through the investigation and after interviewing the man who has been charged."
