To add quotes and details

By Stephen Scheer, Steve Holland, and Parisa Hafezi

JERUSALEM/WASHINGTON/DUBAI, June 18 (Reuters) - Thousands of people are fleeing Tehran and other major cities, Iranian media reported, as Iran and Israel exchanged fresh missile strikes despite U.S. President Donald Trump's call for Iran to surrender unconditionally.

The Israeli military said two barrages of Iranian missiles were fired toward Israel in the first two hours of Wednesday morning. Explosions were heard in the skies over Tel Aviv.

Israel asked residents of an area southwest of the capital, Tehran, to evacuate so its air force could strike military installations. Iranian media reported that thousands fled the capital and other major cities, causing traffic jams and road closures.

The semi-official Mehr news agency reported that clashes broke out in the early hours of Wednesday between security forces and unidentified gunmen in the city of Ray, south of Tehran.

The agency added that the militants were "individuals believed to be linked to Mossad or Israeli spies," and indicated that they planned to "carry out terrorist operations in densely populated areas of the capital."

Iranian news websites reported that Israel also attacked a university linked to Iran's Revolutionary Guard in the east of the country and the Khojir ballistic missile facility near Tehran, which was also targeted by Israeli airstrikes in October.

An Israeli military official said that 50 fighter jets struck approximately 20 targets in Tehran last night, including sites for the production of raw materials, components, and missile manufacturing systems.

The Office of the Director of National Intelligence estimates that Iran is armed with the largest number of ballistic missiles in the Middle East. Iran says its ballistic missiles are an important deterrent and retaliatory force against the United States, Israel, and other potential targets in the region .

Trump warned on social media on Tuesday that the United States' patience was running out. While he said there was no intention of killing Iranian Supreme Leader Ayatollah Ali Khamenei "at this time," his comments signaled a more hawkish stance toward Iran as he considers whether to increase U.S. intervention.

He said on his Truth Social platform that Khamenei's whereabouts are known, but "we will not eliminate him, at least not for now," adding, "Our patience is running out."

Three minutes later, he wrote in a new post, "Unconditional surrender!"

Trump's contradictory and sometimes ambiguous messages about the conflict between Israel, a close US ally, and its archenemy Iran have fueled the uncertainty surrounding the crisis. His public comments have ranged from military threats to diplomatic initiatives, not uncommon for a president known for his erratic approach to foreign policy.

A source familiar with the internal discussions said that Trump and his team are considering a number of options, including joining Israel in striking Iranian nuclear sites .

A White House official said Trump spoke by phone with Israeli Prime Minister Benjamin Netanyahu on Tuesday.

A White House official said Trump met for 90 minutes with the National Security Council on Tuesday afternoon to discuss the conflict. The results of the meeting are not yet clear.

Three US officials told Reuters that the United States is deploying more fighter jets to the Middle East and expanding the deployment of other warplanes. The United States has so far taken only defensive measures in the current conflict with Iran, including helping shoot down missiles fired toward Israel.

A source familiar with US intelligence reports said that Iran has moved some of its ballistic missile launchers, but it is difficult to determine whether they are targeting US forces or Israel.

But British Prime Minister Keir Starmer, speaking at the G7 summit in Canada that Trump left early , said there was no indication the United States was about to intervene in the conflict.

* Weak influence in the region

Five sources familiar with Khamenei's decision-making process said the killing of close military and security advisors in Israeli airstrikes has created significant disruption within his inner circle and increased the risk of strategic miscalculations.

With Iranian leaders facing the most severe security breach since the 1979 revolution that ousted the US- backed Shah and brought clerics to power, Fars News Agency reported that Iran's cybersecurity command has banned officials from using telecommunications devices and mobile phones.

Iranian media reported that Israel launched a "large-scale cyber war" against Iran's digital infrastructure.

Since the attack by the Tehran-backed Palestinian Islamic Resistance Movement (Hamas) on Israel on October 7, 2023, and the outbreak of war in the Gaza Strip , Khamenei's influence in the region has begun to weaken as Israel has pounded the positions of Iran's allies , including the Palestinian Islamic Resistance Movement ( Hamas ) in the Gaza Strip , Hezbollah in Lebanon, the Houthi group in Yemen, and armed factions in Iraq, in addition to the ouster of Iran's close ally, Bashar al-Assad, from power in Syria .

Israel launched its largest- ever air war on Iran on Friday after saying it had concluded Tehran was on the verge of developing a nuclear weapon.

Iran denies seeking nuclear weapons and has stated its right to possess nuclear technology for peaceful purposes, including uranium enrichment, as a member of the Nuclear Non-Proliferation Treaty.

Israel, which is not a party to the treaty, is the only country in the Middle East widely believed to possess nuclear weapons. Israel has neither confirmed nor denied this.

Israeli Prime Minister Benjamin Netanyahu has stressed that he will not back down until Iran halts its efforts to develop nuclear weapons, while Trump says the Israeli attack could end if Iran agrees to strict limits on enrichment.

Before the Israeli attack began, the Board of Governors of the UN's International Atomic Energy Agency said that Iran was violating its nuclear nonproliferation obligations for the first time in nearly 20 years.

The agency reported on Tuesday that there were indications of direct impacts on the underground enrichment halls at the Natanz facility.

Israel announced that it currently controls Iranian airspace and intends to escalate its campaign in the coming days.

But Israel would have difficulty delivering a knockout blow to deep nuclear sites like Fordo, dug beneath a mountain, without the United States joining the attack.

Iranian officials announced the deaths of 224 people, most of them civilians, while Israel said about 24 people were killed. The conflict prompted residents on both sides to flee or evacuate sites that might be targeted.

Global oil markets are on high alert following the strikes targeting sites including the world's largest gas field, South Pars, which Iran shares with Qatar.

(Prepared by Mahmoud Salama and Salma Najm for the Arabic Bulletin - Edited by Mahmoud Reda Murad)