By Steve Holland, Andrew Mills and Parisa Hafezi

WASHINGTON/DOHA/ISTANBUL (Reuters) -Israel's military said Iran launched waves of missiles on Tuesday, with emergency services reporting three people killed, hours after U.S. President Donald Trump announced a complete ceasefire between Israel and Iran to end a 12-day war.

Witnesses said they heard explosions near Tel Aviv and Beersheba in southern Israel. Israel's military said six waves of missiles were launched by Iran and Israel's national ambulance service said three people were killed in Beersheba, the first reported deaths in Israel since Trump announced the ceasefire late on Monday.

A senior White House official said Trump had brokered a ceasefire deal in a call with Israeli Prime Minister Benjamin Netanyahu and Israel had agreed so long as Iran did not launch further attacks.

"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.

An Iranian official earlier confirmed that Tehran had agreed to a ceasefire, but the country's foreign minister said there would be no cessation of hostilities unless Israel stopped its attacks.

Abbas Araqchi said early on Tuesday that if Israel stopped its "illegal aggression" against the Iranian people no later than 4 a.m. Tehran time (0030 GMT) on Tuesday, Iran had no intention of continuing its response afterwards.

"The final decision on the cessation of our military operations will be made later," Araqchi added in a post on X.

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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.

Iran's semi-official SNN news agency reported on Tuesday that Tehran fired its last round of missiles before the ceasefire came into effect.

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

Iran denies ever having a nuclear weapons program but Supreme Leader Ali Khamenei has said that if it wanted to, world leaders "wouldn't be able to stop us".

Israel, which is not a party to the international Non-Proliferation Treaty, is the only country in the Middle East believed to have nuclear weapons. Israel does not deny or confirm that.

Qatar's Prime Minister Sheikh Mohammed bin Abdulrahman Al Thani secured Tehran's agreement during a call with Iranian officials, an official briefed on the negotiations told Reuters on Tuesday.

U.S. Vice President JD Vance, Secretary of State Marco Rubio and U.S. special envoy Steve Witkoff were in direct and indirect contact with the Iranians, a White House official said.

Neither Iran’s U.N. mission nor the Israeli embassy in Washington responded to separate requests for comment from Reuters.

Hours earlier, three Israeli officials had signaled Israel was looking to wrap up its campaign in Iran soon and had passed the message on to the United States.

Netanyahu had told government ministers whose discussions ended early on Tuesday not to speak publicly, Israel's Channel 12 television reported.

Markets reacted favorably to the news.

S&P 500 futures rose 0.4% late on Monday, suggesting traders expect the U.S. stock market to open with gains on Tuesday.

U.S. crude futures fell in early Asian trading hours on Tuesday to their lowest level in more than a week after Trump said a ceasefire had been agreed, relieving worries of supply disruption in the region.

END TO THE FIGHTING?

There did not appear to be calm yet in the region.

The Israeli military issued two evacuation warnings in less than two hours to residents of areas in the Iranian capital Tehran, one late on Monday and one early on Tuesday.

Israeli Army radio reported early on Tuesday that alarms were activated in the southern Golan Heights area due to fears of hostile aircraft intrusion.

Earlier on Monday, Trump said he would encourage Israel to proceed towards peace after dismissing Iran's attack on an American air base that caused no injuries and thanking Tehran for the early notice of the strikes.

He said Iran fired 14 missiles at the U.S. air base, calling it "a very weak response, which we expected, and have very effectively countered."

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Iran's handling of the attack recalled earlier clashes with the United States and Israel, with Tehran seeking a balance between saving face with a military response but without provoking a cycle of escalation it can't afford.

Iran's attack came after U.S. bombers dropped 30,000-pound bunker-buster bombs on Iranian underground nuclear facilities at the weekend, joining Israel's air war.

Much of Tehran's population of 10 million has fled after days of bombing.

The Trump administration maintains that its aim was solely to destroy Iran's nuclear program, not to open a wider war.

"Iran was very close to having a nuclear weapon," Vice President JD Vance said in an interview on Fox News' "Special Report with Bret Baier."

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

Trump has cited intelligence reports that Iran was close to building a nuclear weaopon, without elaborating. However, U.S. intelligence agencies said earlier this year they assessed that Iran was not building a nuclear weapon and a source with access to U.S. intelligence reports told Reuters last week that that assessment hadn't changed.

In a social media post on Sunday, Trump spoke of toppling the hardline clerical rulers who have been Washington's principal foes in the Middle East since Iran's 1979 Islamic Revolution.

Israel, however, had made clear that its strikes on Evin prison - a notorious jail for housing political prisoners - and other targets in Tehran were intended to hit the Iranian ruling apparatus broadly, and its ability to sustain power.

(Additional reporting by Howard Goller, Humeyra Pamuk, Noel Randewich, Jeff Mason, Enas Alashray, Yomna Ehab, Bhargav Acharya, Jasper Ward and Kanishka Singh; Writing by Costas Pitas and Stephen Coates; Editing by Michael Perry and Lincoln Feast)

Posted by: Aangeles