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

Israel has begun flying home citizens stranded overseas, launching a phased airlift operation on Wednesday following the country’s unexpected military strike on Iran that left tens of thousands of Israelis stuck abroad.

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

"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.

According to the transport ministry, more than 50,000 Israeli citizens are currently attempting to return home. El Al has scheduled additional repatriation flights from Athens, Rome, Milan and Paris. Smaller Israeli airlines Arkia and Israir are also participating in the coordinated effort.

Tel Aviv’s Ben Gurion Airport has been closed to passenger departures since Israel launched its attack on Friday.

Iran has since fired more than 400 ballistic missiles, with many targeting the Tel Aviv area. At least 24 people have died in the strikes.

The Airports Authority has reinforced staffing to help process returning passengers quickly. 

Travellers were shuttled to their parked vehicles or transported to city centres by train and bus. Authorities advised relatives not to come to the airport for security reasons.

A spokesperson for the Airports Authority said the airlift is being carried out in phases based on risk levels and security assessments, with safety prioritised for all passengers, flight crews, and aircraft.

With no outbound passenger flights operating from Israel, around 40,000 tourists remain stranded inside the country. El Al has cancelled all scheduled departures through to 23 June.

Meanwhile, Cyprus, the closest European Union member state to Israel, has become a key transit point for returnees. 

Nine flights from Larnaca to Haifa and four to Tel Aviv were expected to operate on Wednesday, carrying about 1000 passengers, according to officials from Cypriot airport operator Hermes. 

Cruise operator Mano Maritime also announced that its ship “Crown Iris,” with a capacity of 2,000 passengers, will make two crossings from Cyprus to Israel’s Mediterranean port city of Haifa.

Earlier on Wednesday, a cruise ship carrying 1,500 participants of a Jewish heritage programme arrived in Cyprus after departing Israel on Tuesday.