The Foreign Office confirmed that two flights had left the country, with further flights expected in the days ahead.
One flight was a commercial charter flight, while an RAF A400M transport plane was also used.
It is expected that the Ministry of Defence will continue to play a role supporting the Foreign Office in the charter effort.
Foreign Secretary James Cleverly, in a post on X, said: “The UK is continuing to help vulnerable British nationals leave Israel.
“Two charter flights have now left Israel and we expect more to leave in the coming days.
“It’s more important than ever that you follow our travel advice and register your presence.”
The UK Government had initially 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 originally 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.
A Government spokesperson said: “Two flights facilitated by the UK Government have now departed Israel. Further flights are expected to leave in the coming days while commercial options are limited.”
Several airlines have suspended their flights between Israel and the UK, including British Airways, Virgin Atlantic, easyJet and Wizz Air.