President Mahmoud Ahmadinejad issued the order in reaction to the UN nuclear watchdog's decision to report Iran to the UN Security Council.
In a letter to the chief of Iran's Atomic Energy Organisation, Gholamreza Aghazadeh, the president ordered an end to the implementation of the additional protocol of the nuclear Non-Proliferation Treaty (NPT).
"As of Sunday, the voluntary implementation of the additional protocol and other cooperative measures beyond the NPT must be suspended according to the law," Ahmadinejad said.
The order was issued shortly after an emergency meeting of IAEA board of governors adopted a resolution to report Iran's nuclear issue to the UN Security Council.
The additional protocol, signed by the Iranian government in December 2003, but never ratified by the Iranian parliament, allowed snap inspections of nuclear sites by the International Atomic Energy Agency (IAEA).
The parliament passed a law last November which requires the government to cease all voluntary confidence-building measures including implementation of the additional protocol if the country's nuclear case was referred to the UN Security Council.
Ahmadinejad said that Iran would press on with research and development of nuclear technology and prepare to use it for peaceful purposes.
He said that all peaceful nuclear activities would be carried out within the framework of the IAEA regulations, the NPT clauses and the Safeguard Agreement.
The hardline president said the IAEA's resolution was adopted under the pressure of "certain countries".
The dispute over Iran's nuclear programme has intensified since it resumed nuclear fuel research on January 10, despite warnings by the European Union.
The EU has been negotiating with Iran for two years, but broke off the talks after Iran restarted uranium conversion, a precursor to enriching uranium into fuel, last August.
The EU has been trying to persuade Iran to give up uranium enrichment which can be used to fuel power plants or make atom bombs.
The United States has accused Iran of secretly developing nuclear weapons.
Iran has rejected the charge, insisting that its nuclear programme is for peaceful purposes and aimed at meeting rising domestic demand for electricity.