The RAF flight carried passengers from Israel to Cyprus last night.
It is understood that the air force is assisting the Foreign Office due to the current limited availability of commercial flights.
A Royal Air Force A400M made two flights from Tel Aviv to Cyprus, the first on Friday night and the second during the early hours of Saturday morning, according to FlightRadar24.
A Foreign Office (FCDO) statement earlier said: “A UK Government charter flight has now left Israel (October 13), with further flights expected to leave in the coming days while commercial options are limited.”
It comes as the UK Government had failed to organise repatriation flights from Israel due to problems obtaining insurance, an aviation source told the PA news agency.
A UK-organised flight was initially planned to arrive at Gatwick Airport on Friday, but that was cancelled amid the ongoing Israel-Hamas conflict.
An attempt to arrange a flight landing at the West Sussex airport at 5.40pm on Friday also failed.
PA understands one of the reasons for the lack of flights is that Titan Airways, the contracted airline, was having difficulties arranging insurance.
The airline was approached for comment.
A spokeswoman for the FCDO said earlier: “This is a fluid situation and we are currently working to ensure the flight can proceed as soon as possible.”
Other options include scheduled services to Heathrow and Luton airports by Israeli airline El Al and a repatriation flight to Heathrow for Australian nationals organised by the country’s government and operated by Qantas.
Several airlines have suspended their flights between Israel and the UK, including British Airways, Virgin Atlantic, easyJet and Wizz Air.
When the FCDO announced on Thursday it would organise flights, it said the first one would operate that day and they will be available to “British nationals, including dual nationals, and dependants if travelling with a British national normally resident in the UK”.
Each ticket will cost £300, which “reflects the costs of operating the flight”, according to the FCDO.
The children and other dependants of British diplomats will be given seats as “we have a duty of care to our staff”, it added.