AFP journalists heard violent, sustained explosions in Jerusalem and Tel Aviv, and sirens sounded in several parts of the country to warn of incoming Iranian missiles.
Shortly afterwards, the army said citizens could leave their shelters, while the foreign minister said the Soroka hospital in southern Israel's Beersheba had suffered "extensive damage" in a strike.
Israeli rescuers said at least 32 people were injured in Iran's latest missile attack.
The explosions in Jerusalem were the loudest heard by AFP journalists since the conflict began last week. The barrage came after fresh Israeli strikes on Tehran and elsewhere, and with growing speculation about whether Washington would enter the fray.
Iran's supreme leader Ayatollah Ali Khamenei meanwhile rejected Trump's demand for an "unconditional surrender", despite claims from the US leader that "Iran's got a lot of trouble and they want to negotiate".
Trump has left his intentions on joining the conflict deliberately ambiguous, saying Wednesday: "I may do it, I may not do it. I mean, nobody knows what I'm going to do."
"The next week is going to be very big," he added, without further details.
- 'Never surrender' -
The White House said Trump would receive an intelligence briefing on Thursday, a US holiday. Top US diplomat Marco Rubio is set meet his British counterpart for talks expected to focus on the conflict.
"I have ideas as to what to do, but I haven't made a final (decision)," Trump said. "I like to make the final decision one second before it's due, because things change. Especially with war."
The Wall Street Journal reported that Trump had told aides on Tuesday he had approved attack plans but was holding off to see if Iran would give up its nuclear programme.
Trump told reporters that Iranian officials "want to come to the White House", a claim denied by Tehran.
The US president had favoured a diplomatic route to end Iran's nuclear programme, seeking a deal to replace the 2015 agreement he tore up in his first term.
But since Israel unleashed the campaign against Iran one week ago, Trump has stood behind the key US ally.
The United States is the only country with the "bunker buster" bombs needed to destroy Iran's Fordow nuclear plant, but US military action is deeply unpopular with parts of Trump's base.
Khamenei on Wednesday insisted Iran "will never surrender", and called Trump's ultimatum "unacceptable".
"America should know that any military intervention will undoubtedly result in irreparable damage," Khamenei added.
- Dozens killed -
On Thursday morning, Israel said it was carrying out fresh strikes on Tehran and other parts of Iran, and warned civilians in two villages, Arak and Khondab, to leave ahead of new attacks.
An Israeli military official, who asked not to be named, said Wednesday that Iran had fired around 400 ballistic missiles and 1,000 drones since the conflict began on Friday.
About 20 missiles had struck civilian areas in Israel, the official added.
Iranian strikes have killed at least 24 people and injured hundreds since they began, Israeli Prime Minister Benjamin Netanyahu's office said on Monday.
Iran said Sunday that Israeli strikes had killed at least 224 people, including military commanders, nuclear scientists and civilians.
Both countries have not issued an updated official toll since then.
Israel says its surprise air campaign is aimed at preventing Iran from acquiring nuclear weapons.
Iran had been enriching uranium to 60 percent -- far above the 3.67-percent limit set by the 2015 nuclear death but still short of the 90-percent threshold needed for a nuclear warhead.
Israel has maintained ambiguity on its own atomic activities, but the Stockholm International Peace Research Institute says it has 90 nuclear warheads.
- 'Immediate de-escalation' -
Israel's strikes have prompted mass evacuations and food and fuel shortages in Iran.
"There are shortages of rice, bread, sugar and tea," a 40-year-old Iranian driver told AFP at the Iraqi border crossing of Bashmakh, seeking anonymity for fear of reprisals.
There was also a "near-total national internet blackout" in Iran on Wednesday, a London-based watchdog said, with Iran's Fars news agency confirming heavier internet restrictions after initial curbs imposed last week.
The military campaign has sparked calls for a return to diplomacy.
Russian President Vladimir Putin said Thursday that a deal to guarantee both Israel's security and Iran's desire for a civilian nuclear programme was possible.
"I believe it would be good for all of us together to look for ways to stop the fighting and seek ways for the participants in the conflict to find an agreement," he told foreign journalists at a televised event.
He said Iran had not asked Russia for military help.
Iran's Foreign Minister Abbas Araghchi said his country remains committed to diplomacy, noting Iran "has so far only retaliated against the Israeli regime and not those who are aiding and abetting it".
But there were lingering questions about how the conflict could evolve, with Trump telling reporters that a change in Iran's government "could happen", a day after he had boasted that Washington could assassinate Khamenei, but would not, "at least not for now".
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