US President Donald Trump said on Tuesday a ceasefire between Israel and Iran was now in place and asked both countries not to violate it, only hours after Iran launched waves of missiles, which Israel's ambulance service said killed four people.

"THE CEASEFIRE IS NOW IN EFFECT. PLEASE DO NOT VIOLATE IT!" Trump said in a Truth Social post.

When Trump announced on Monday what he called a complete ceasefire to end a 12-day war, 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.

Israel's military said six waves of missiles were launched by Iran and Israel's national ambulance service said four people were killed in Beersheba, the first reported deaths in Israel since Trump announced the ceasefire.

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

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 4am Tehran time, or 8.30am Hong Kong time, 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. 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 programme 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 said on Tuesday. (Reuters)