Iran's supreme leader Ayatollah Ali Khamenei explicitly endorsed a nuclear deal with world powers for the first time Wednesday, but warned his president it contained weaknesses that must be guarded against.

Despite years of negotiations that culminated in a July 14 accord, Khamenei had never before said openly that he backed the diplomacy. Nor had he said he was against talks.

The agreement with the five permanent members of the UN Security Council plus Germany will see a raft of trade sanctions against Iran lifted in return for curbs lasting up to 15 years on its atomic activities.

After years of tension and Western sanctions, which have ravaged Iran's economy, Khamenei permitted secret talks on the nuclear issue with the United States, which commenced in Oman in 2012.

But the process only gained momentum and became official, involving Britain, China, France, Russia and the US plus Germany, after Iranians elected President Hassan Rouhani, a relative moderate, in June 2013.

The supreme leader's remarks on the final nuclear deal came in a letter to Rouhani a week after Iran's parliament approved it, after months of often fierce opposition from hardliners angered by what they said were too many concessions.

Khamenei, who has the last word for Iran on all policy matters, said he had approved the decision of the country's top security committee, the Supreme National Security Council (SNSC), to implement the agreement.

- Warning on breaches -

However he told Rouhani the deal had "many ambiguities and structural weak points" which must be closely monitored.

"In the absence of tight control these could bring significant damage for the present and the future of the country," Khamenei said of such shortcomings, repeating his long-held stance that the United States cannot be trusted.

A committee, controlled by the SNSC, will be formed to monitor "possible breaches and deception by the other parties, in particular the US" he said in the letter, which was published on his website.

Iran has always denied pursuing an atomic weapon but Western intelligence agencies alleged that work to develop a bomb had taken place.

The lifting of sanctions is conditional on Iran putting stringent curbs on its nuclear programme, including on its enrichment of uranium, the processing of which at high purity can produce bomb material.

The main provisions of the agreement, known as the Joint Comprehensive Plan of Action (JCPOA), extend for between eight to 15 years.

Khamenei said any new sanctions against Iran would be a fatal breach.

If such occurred "under any pretext by any country engaged in negotiations, it will be a violation of the JCPOA and the government will be obligated to stop the agreement," the 76-year-old leader said.

On Sunday, US President Barack Obama and the European Union announced measures to ensure the lifting of sanctions, including those on Iran's banks and energy sector, as soon as international monitors complete a probe into possible military dimensions of Tehran's past nuclear activities.

- IAEA probe due December 15 -

The UN nuclear watchdog, the International Atomic Energy Agency (IAEA) is due to submit that report by December 15. The deal's crucial "implementation day" can only happen after.

Khamenei said the IAEA investigation must be closed before Iranian officials will take steps to ensure its Arak reactor cannot produce plutonium -- another potential route to an atomic weapon.

China has agreed to work with Iran and the United States to alter the Arak reactor, officials have said.

Another condition of the deal -- that Iran's stockpile of low-enriched uranium be exported out of the country -- also cannot go ahead until the IAEA has completed its investigation, Khamenei stipulated.

Iran has also agreed to disable more than two-thirds of its 19,000 centrifuges -- fast-spinning machines that enrich uranium -- with just over 6,000 being left in place.

The nuclear agreement, which has brought Iran out of the diplomatic cold after years of high tension on the nuclear issue, raised expectations of further detente.

However, Khamenei has since banned other negotiations with the United States, Iran's main adversary since the Islamic revolution toppled the US-backed shah in 1979.

The supreme leader's letter to Rouhani reiterated the point.

"You know the US government had an attitude of hostility. They are unlikely to change their attitude in the future," Khamenei wrote.