In retaliation over the reporting of Iran's disputed atomic drive to the UN Security Council, on Saturday the Iranian president also called for "preparations" to kick-start ultra-sensitive uranium enrichment work, the focus of fears that Iran could acquire nuclear weapons.
"As of tomorrow (Sunday), the voluntary application of the additional protocol and all measures beyond it will cease," Ahmadinejad wrote in a letter to the head of the Iranian Atomic Energy Organisation.
The additional protocol to the nuclear Non-Proliferation Treaty (NPT) was signed by Iran's former reformist government but never ratified by the parliament.
It gives the IAEA stronger inspection powers and is seen as crucial to efforts to establish the nature of the Islamic republic's nuclear activities.
Ahmadinejad also said it was "necessary to take action to implement" a law passed by parliament, which also called for a resumption of all nuclear activities that had been suspended as part of deals with Britain, France and Germany.
But the president appeared to stop short of ordering an immediate resumption of uranium enrichment - a process that makes reactor fuel but which can also be extended to make the fissile core of a nuclear bomb.
In the letter Ahmadinejad wrote: "The activities of research and development and the preparation for the use of nuclear fuel technology for peaceful purposes must be seriously and concertedly put into action."
Gholam Reza Aghazadeh, the head of Iran's Atomic Energy Organisation, and Iran's vice president, told state television he would "take the necessary measures to carry out the president's order".
But while vowing retaliation, he also asserted Iran was willing to negotiate.
"We are ready to negotiate with every country with the exception of Israel and which recognises our right"
Gholam Reza Aghazadeh,
Head of Iran's Atomic Energy Organisation
He said: "We have not left the NPT and we will not leave the NPT. We are ready to negotiate with every country with the exception of Israel and which recognises our right."
Recent Iranian offers for talks have been rejected in the West, which first wants Iran to return to a suspension of its nuclear fuel work.
Aghazadeh said: "Even though there is an unjust resolution, we are ready to negotiate with the Europeans."
Ahmadinejad also condemned the resolution, passed earlier on Saturday by the IAEA's 35-nation board of governors.
He wrote: "The board of governors, under the influence of certain countries and without any international legal or judicial justification, adopted a resolution which does not take into account Iran's extensive cooperation and which violates the national rights of Iran."
Aside from reporting Iran to the Security Council - which leaves Tehran exposed to the threat of sanctions - the resolution also called on the country to return to a full suspension of enrichment-related work, ratify the additional protocol and "extend full and prompt cooperation" to the IAEA, already deemed "indispensable and overdue".
Iran insists it only wants to generate electricity, and argues fuel cycle work is a right enshrined by the NPT.