Kharazi, speaking to reporters after meetings with Prime Minister Helen Clark and Foreign Minister Phil Goff, reiterated that his country is not producing nuclear weapons.
"It is our legitimate right to have nuclear technology for peaceful purposes," he said.
If Israel attacked the facilities, Iran would react.
"We have our defence capability and that certainly keeps others from exercising such a threat," he said.
Iran has been resisting cooperation with the United Nations nuclear watchdog, the International Atomic Energy Agency (IAEA), which has been investigating the possibility that Tehran is hiding another nuclear site.
New Zealand is on the board of the IAEA and Clark said Kharazi's visit was important because Iran's nuclear programme was occupying a lot of the agency's time.
"We have at a diplomatic level kept a dialogue with Iran about its nuclear programme and of course we're aware that Iran's senior leaders have given assurances that their intentions are to develop a programme for peaceful purposes only," she said.
"However, you would have to be concerned at the length of time which it is taking for the IAEA to be able to get to the bottom of what exactly it is that Iran is actually doing," Clark said.