Israel began flying home citizens stranded abroad on Wednesday, launching a phased airlift operation after the country's surprise military strike on Iran left tens of thousands of Israelis stuck overseas.

The first rescue flight, operated by national carrier El Al, touched down at Ben Gurion Airport early Wednesday morning, bringing home passengers from Larnaca, Cyprus.

Worldwide, Israel's transport ministry estimates that more than 50,000 stranded Israelis are trying to come home.

El Al has said repatriation flights are already scheduled from Athens, Rome, Milan and Paris. Smaller rivals Arkia and Israir are also taking part in the operation.

"We are preparing for the airlift to bring all Israelis home," Transportation Minister Miri Regev told the captain of the arriving El Al flight before it landed, according to a statement released by the Israeli Aviation Authority.

"We are very emotional about receiving the first rescue flight as part of 'Safe Return'. Land safely," she added.

Tel Aviv's airport has been closed to passenger traffic since Israel launched its attack on Friday.

The Airports Authority reinforced staffing on Wednesday to ensure the arriving passengers exited the airport quickly. They were shuttled to their parked vehicles or transported via train and bus to city centres nationwide.

The operation is being carried out in stages, based on risk levels and security assessments, with an emphasis on the safety of passengers, flight crews, and aircraft, a spokesperson for the airports authority said.

Relatives were advised to avoid travelling to airports for security reasons.

Iran has fired more than 400 ballistic missiles at Israel since Friday, a large number of them targeting the Tel Aviv area. At least 24 people have died so far in the strikes.

There are still be no passenger flights leaving Israel, meaning up to 40,000 tourists are stranded in the country. El Al has cancelled all scheduled flights through to June 23.

Large numbers of Israelis seeking to get home have converged on Cyprus, the European Union member state closest to Israel. Flights from the coastal city of Larnaca to Tel Aviv take 50 minutes.

Nine flights were expected to depart Cyprus Wednesday for Haifa, and four for Tel Aviv, carrying about 1,000 people, sources in the Cypriot airport operator Hermes said.

Cruise operator Mano Maritime, whose "Crown Iris" ship carries 2,000 passengers, has said it will make two crossings from Cyprus to Israel's Mediterranean port city of Haifa.

Earlier on Wednesday, a cruise ship arrived in Cyprus carrying 1,500 participants to a Jewish heritage programme who had left Israel on Tuesday.