There had been a call from the chair of a group called the Bougainville Hardliners, James Onartoo, who said the government in the autonomous Papua New Guinea province needed to explain "what these police were up to", Radio New Zealand International reported.
Onartoo said the AFP officers and civilian staff appeared to be taking GPS readings at the site of the defunct Panguna copper-gold mine site in central Bougainville.
But Tokura says they were there as part of preparations for the international police support team that will be in Bougainville at the time of its referendum on independence in October.
That mission, to be led by New Zealand, will also include police from Fiji, Solomon Islands and Australia.
The AFP has been harshly criticised in Australia lately for what has been perceived as its high-handed harrassment of media institutions in that country.