Secret operations were launched by Israeli Mossad commandos deep inside Iran ahead of the wave of attacks on Tehran’s nuclear and missiles sites, say security sources.
The covert missions included establishing an attack-drone base near the Iranian capital.
Analysis: Israel's strike on Iran will have perilous consequences for us all
The security source said precision-guided weapons were deployed in open areas near Iranian surface-to-air missile systems sites.
Advanced technology was also used to target Iran's air defence systems.
The secret infiltration raids were part of major strikes launched by Israel against Iran on Friday, saying it had targeted nuclear facilities, ballistic missile factories and military commanders at the start of a prolonged operation to prevent Tehran from building an atomic weapon.
The Israeli military said it had carried out a large-scale strike against Iran's air defences, destroying "dozens of radars and surface-to-air missile launchers".
Iranian media and witnesses reported explosions including at the main uranium enrichment facility at Natanz.
Iran's elite Revolutionary Guards Corps said its top commander, Hossein Salami, had been killed and state media reported the unit's headquarters in Tehran had been hit.
Several children were killed in a strike on a residential area in the capital, they said.
The chief of staff of the Iranian armed forces, General Mohammad Bagheri, was also confirmed dead by Iranian state television.
Iran’s Supreme Leader Ayatollah Ali Khamenei warned “severe punishment” would be directed at Israel. which said it was working to intercept about 100 drones launched towards its territory in retaliation.
But around 0800 GMT, Israeli media said an order to citizens to remain near protected areas had been lifted, suggesting that most or all the drones had been neutralised.
The price of crude oil leapt on fears of retaliatory attacks on a major oil producing region, but then eased back somewhat.
"We are at a decisive moment in Israel's history," Israeli Prime Minister Benjamin Netanyahu said in a recorded video message.
"Moments ago, Israel launched Operation Rising Lion, a targeted military operation to roll back the Iranian threat to Israel's very survival."
The International Atomic Energy Agency said there was no increase in radiation levels at the Natanz nuclear site, citing information provided by Iranian authorities.
Before chairing a meeting of his National Security Council, Donald Trump urged Iran to make a deal over its nuclear programme, saying that there was still time for the country to prevent further conflict with Israel.
"There has already been great death and destruction, but there is still time to make this slaughter, with the next already planned attacks being even more brutal, come to an end," Trump said in a post on Truth Social.
Flights from Heathrow to Tel Aviv were suspended on Friday and airlines quit the airspace over Israel, Iran, Iraq and Jordan as the war between the two Middle East enemies exploded.
The Israeli military said it had been forced to act by new intelligence information showing that Iran was "approaching the point of no return" in the development of a nuclear weapon.
But a source familiar with US intelligence reports said there had been no recent change in America’s assessment that Iran was not building a nuclear weapon.
