Iranian and Israeli media have reported new Israeli airstrikes on Iran, despite US President Donald Trump's statement that Israel called them off at his command to preserve an hours-old ceasefire.

Two explosions were heard in the capital, the judiciary news outlet Mizan reported. Israeli army radio said Israel had struck an Iranian radar site near Tehran.

The strikes took place minutes after Trump said Israel had called off its attack in response to his command.

"All planes will turn around and head home, while doing a friendly 'Plane Wave' to Iran. Nobody will be hurt, the Ceasefire is in effect!" Trump said in a post on Truth Social.

Trump had earlier accused both Israel and Iran of violating the ceasefire, while expressing particular frustration with Israel which had announced major new strikes on Tehran.

The Israeli city of Beersheba was hit by Iran before the ceasefire was supposed to be in affect. - AP

"Israel. Do not drop those bombs. If you do it it is a major violation. Bring your pilots home, now!" Trump wrote on Truth Social shortly after he left the White House for a trip to a NATO summit in The Hague.

Before boarding, he told reporters he was "not happy" with either side for violating the truce, particularly with Israel.

"I've got to get Israel to calm down now," Trump said as he left the White House.

"Israel, as soon as we made the deal, they came out and they dropped a load of bombs, the likes of which I've never seen before, the biggest load that we've seen."

Iran and Israel had been fighting "so long and so hard that they don't know what ... they're doing," he said before turning away from cameras and heading to his helicopter.

Earlier, Israeli Defence Minister Israel Katz had said he had ordered the military to mount new strikes on targets in Tehran in response to what he said were Iranian missiles fired in a "blatant violation" of the ceasefire.

Iran denied launching any missiles and said Israel's attacks had continued for an hour and a half beyond the time the ceasefire was meant to start.

Drone video shows rescue efforts, destruction after Iranian missile strike in Beersheba. - Reuters

The developments raised early doubts about the ceasefire, intended to end 12 days of war.

Katz said in a statement he had ordered the military to "continue high-intensity operations targeting regime assets and terror infrastructure in Tehran" in light of "Iran’s blatant violation of the ceasefire declared by the President of the United States".

Hours earlier, Trump had posted on Truth Social:

"THE CEASEFIRE IS NOW IN EFFECT. PLEASE DO NOT VIOLATE IT!"

Both Israel and Iran had confirmed the ceasefire after Trump's announcement.

Israeli Prime Minister Benjamin Netanyahu had said his country had achieved the goals it set in launching its June 13 surprise attack on Iran - to destroy its nuclear programme and missile capabilities.

"Israel thanks President Trump and the United States for their support in defense and their participation in eliminating the Iranian nuclear threat," Netanyahu had said.

Iran's Foreign Minister Abbas Araqchi had said that Iran would halt its retaliatory strikes provided that Israel stopped attacking as of 4 am in Tehran.

In the last reported strikes before the ceasefire, missiles killed four people in the southern Israeli city of Beersheba, the Israeli ambulance service said. Iranian officials said nine people including a nuclear scientist were killed in a strike on a residential building in northern Iran.

Rescuers in southern Israel search for people trapped after Iranian missile barrage. - AP

When Trump announced the ceasefire, he appeared to suggest that Israel and Iran would have time to complete missions that were underway, at which point the ceasefire would begin in a staged process.

Witnesses said they heard explosions near Tel Aviv and Beersheba in southern Israel before Trump's statement.

Iranian state television announced the ceasefire in a graphic on screen, not immediately acknowledging the new missile barrage coming after the deadline set by Trump.

A series of Iranian barrages before the ceasefire deadline killed three people and injured at least eight others, Israel’s Magen David Adom rescue services said. At least one person was believed trapped in the rubble and a residential building in Israel’s south sustained heavy damage, according to emergency services.

It is unknown if these barrages played a part in the continued strikes after the ceasefire confirmations.

Trump's announcement of a “complete and total ceasefire" came soon after Iran launched a limited missile attack Monday on a US military base in Qatar, retaliating for the American bombing of its nuclear sites. Israel has not acknowledged the Trump ceasefire announcement.

Aftermath of Iran's strike on Israel. – Reuters

The US President's subsequent post on Truth Social said the ceasefire beginning about midnight Washington time would bring an “Official END” to the war.

Israel did not immediately acknowledge any ceasefire, but there were no reports of Israeli strikes in Iran after 4am in Tehran. Heavy Israeli strikes continued in Iranian cities until shortly before that time. Israel in other conflicts has stepped up its strikes just before ceasefires took effect.

"On the assumption that everything works as it should, which it will, I would like to congratulate both Countries, Israel and Iran, on having the Stamina, Courage, and Intelligence to end, what should be called, 'THE 12 DAY WAR'," Trump wrote on his Truth Social site.

Israel, joined by the United States on the weekend, had carried out attacks on Iran's nuclear facilities, after alleging Tehran was getting close to obtaining a nuclear weapon.

It’s unclear what role Ayatollah Ali Khamenei, Iran’s leader, played in the talks. He had said on social media earlier Monday that Iran would not surrender. \

"As of now, there is NO ‘agreement’ on any ceasefire or cessation of military operations,” Araghchi wrote on social media.

Iran foreign minister posts about possible ceasefire. – Reuters

“However, provided that the Israeli regime stops its illegal aggression against the Iranian people no later than 4am Tehran time, we have no intention to continue our response afterwards.”

Trump's initial ceasefire announcement came just before he left for a NATO summit in the Netherlands, where he will likely make the case that his mix of aggression and diplomacy has succeeded.

As Trump described it, the ceasefire would start with Iran and then be joined by Israel 12 hours later, with the president writing that the respective sides would “remain PEACEFUL and RESPECTFUL”. The phased-in ceasefire was set to begin Tuesday morning in Israel and Iran and culminate within 24 hours.

“This is a War that could have gone on for years, and destroyed the entire Middle East, but it didn’t, and never will!” Trump said.

Qatar's Prime Minister Sheikh Mohammed bin Abdulrahman Al Thani secured Tehran's agreement during a call with Iranian officials.

An official said Vice President JD Vance, Secretary of State Marco Rubio and special envoy Steve Witkoff communicated with the Iranians through direct and indirect channels.

The White House has maintained that the effectiveness of the US strikes helped get the Israelis to agree to the ceasefire and that the Qatari government helped to broker the deal.

Trump spoke to Qatar's emir, Sheikh Tamim bin Hamad Al Thani, to thank him for helping land the agreement. The Gulf emirate has been chief interlocutor in the on-and-off ceasefire and hostage negotiations between Israel and Hamas in their ongoing war in Gaza.

Trump appeared to suggest that Israel and Iran would have some time to complete any missions that are underway, at which point the ceasefire would begin in a staged process.

Vance said in a TV interview just as the ceasefire was announced that the world would look back at the war between Israel and Iran – and the US bombing of Iran’s nuclear facilities –as “an important reset moment for the entire region”.

Vice President JD Vance speaks on Fox News' Special Report. – AP

Appearing on Fox News Channel's Special Report, the vice president said the Trump administration hoped that the Iranians had learned an important lesson – If they want to build a nuclear weapon in the future, he said, “they’re going to have to deal with a very, very powerful American military again”.

Vance said Iran was no longer able to build a nuclear weapon after US strikes destroyed its infrastructure.

"Iran was very close to having a nuclear weapon," Vance said. "Now Iran is incapable of building a nuclear weapon with the equipment they have because we destroyed it."

White House press secretary Karoline Leavitt posted on social media that Trump “has accomplished what no other president in history could ever imagine – the obliteration of the Iranian Regime’s nuclear program, and an unprecedented ceasefire between Israel and Iran”.

The ceasefire announcement came after Iran attempted to retaliate for the US assault with a Monday missile strike aimed at a major US military installation in the Gulf nation of Qatar. Trump separately thanked Iran on social media for giving the US and allies “early notice” of the retaliation.

The president expressed hope that Tehran — with its reprisal for the US bombardment of three key Iranian nuclear facilities — had "gotten it all out of their ‘system’,” and that the moment would lead to a de-escalation in the Israel-Iran war.

Donald Trump. – Reuters

“I am pleased to report that NO Americans were harmed, and hardly any damage was done,” Trump said on social media. “I want to thank Iran for giving us early notice, which made it possible for no lives to be lost, and nobody to be injured. Perhaps Iran can now proceed to Peace and Harmony in the Region, and I will enthusiastically encourage Israel to do the same."

The Iranian attack on US forces at Qatar’s Al Udeid Air Base marked Tehran's first act of direct retaliation against the US since Trump ordered strikes on Iran’s nuclear facilities.

Leon Panetta, who served as CIA director and defence secretary under former President Barack Obama, said Iran’s restrained response suggests that “their ability to respond has probably been damaged pretty badly”. He also said it’s a potential signal “they’re not interested in escalating the war, either with Israel or the United States”.

Trump said Iran launched 14 missiles at the base, a sprawling facility that hosts the forward headquarters of the US military’s Central Command and was a major staging ground during the US wars in Iraq and Afghanistan. The base houses some 8000 US troops, down from about 10,000 at the height of those wars.

The president said 13 of the Iranian missiles “were knocked down” by US air defence systems while one was “'set free' because it was headed in a nonthreatening direction”.

End to the fighting?

Despite the early threats to the ceasefire, the response across the region and wider world was largely one of relief at the prospect of an end to the biggest direct confrontation ever between the two foes.

Global stock markets surged and oil prices tumbled after the ceasefire announcement, in the hope it heralded a resolution of the war two days after the United States hit Iranian nuclear sites with huge bunker-busting bombs.

"We’re happy, very happy. Who mediated or how it happened doesn’t matter. The war is over. It never should have started in the first place," said Reza Sharifi, 38, heading back to Tehran from Rasht on the Caspian Sea, where he had relocated with his family to escape strikes on the capital.

"I was so worried that Iran would end up like Syria or Iraq," said Maryam, 41, who stayed in Tehran because her family had no money to travel. "I want my two children to grow up in peace. I want them to live their childhood happily."

Fleeing airstrikes, Iranians seek relief in bordering Armenia, Azerbaijan. – AP

Israel attacked on June 13, hitting Iranian nuclear sites and killing the top echelon of its military command in the worst threat faced by the Islamic Republic since war with Iraq in the 1980s.

During the campaign, Israel said it was prepared to topple Iran's clerical rulers if necessary to achieve its aims and struck symbolic targets unrelated to the military, culminating on Monday with a strike on Tehran's Evin prison.

Iranian officials say hundreds of people have been killed in airstrikes. Full information about the extent of the damage cannot be confirmed independently, with media tightly controlled.

Iran's retaliatory missile strikes killed 28 people in Israel, the first time large numbers of Iranian missiles have penetrated its defences.