Sky News understands that the UK’s chief rabbi, Sir Ephraim Mirvis, was aboard the flight as he had been in Israel.
Mr Lammy said the group will be brought home from Cyprus “this evening” and more flights will follow.
He said those with the greatest need will be prioritised and urged all British nationals still in Israel and the occupied territories to register their presence with the UK Foreign Office so they receive updates.
Israel began strikes against Iran earlier this month, claiming Tehran was on the verge of developing nuclear weapons, and has struck nuclear sites, military bases and civilian areas.
Iran insists its nuclear programme is only for peaceful purposes. It has retaliated with missile and drone strikes on Israel.
The UK had not begun evacuating civilians up to this point, saying it had to wait for airspace to open up before planes could be sent.
Image: The site of an Iranian missile strike in Tel Aviv, Israel on Sunday. Pic: AP
Mr Lammy confirmed that one British national in Israel had been injured during Iranian missile attacks and had been offered consular support.
He said it was more difficult to support British nationals in Iran as airspace is closed and there is a “near total internet shutdown”.
Mr Lammy repeated his plea to Iran to return to the negotiating table, after president Masoud Pezeshkian said the US “must receive a response for their aggression”.
“My message for Tehran was clear, take the off ramp, dial this thing down, and negotiate with the United States seriously and immediately,” Mr Lammy said.
“The alternative is an even more destructive and far-reaching conflict, which could have unpredictable consequences.”
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Where does the UK stand on US-Iran strikes?
During the debate, Mr Lammy also faced questions on the legality of the US strikes.
Earlier, Downing Street had said that preventing Iran from obtaining a nuclear bomb was a “good thing” for the UK, but declined to comment on whether the US strikes complied with international law.
The foreign secretary also would not give a position, telling MPs it “must rightly be a matter for the US government in relation to their action” and the UK has been clear “that we were not involved”.
SNP Westminster leader Stephen Flynn accused the foreign secretary of “taking the public for fools” by refusing to answer the question directly, while shadow foreign secretary Dame Priti Patel accused the government of hiding behind “vague language”.
She added: “The British public deserve to know if their government supports degrading the threat of Iran to us and our allies, or whether it is all too happy to sit on the moral fence.”
Qatar shuts its airspace
Amid the continuing conflict, the foreign office has also advised British nationals in Qatar to “shelter in place” following a US security alert.
The advice came moments before Qatar announced it was closing its airspace, which was followed by reports of Iranian missiles targeting US bases there.
Iran later confirmed it had launched attacks on US airbases in Qatar and Iraq.
Israel's ambassador to the UK has insisted children have "never" been targeted in Gaza and said Hamas should be blamed for every death. Tzipi Hotovely was challenged on the deaths of innocent civilians by Wilfred Frost after two British surgeons, who have worked in Gaza during the Israeli bombardment, filmed video blogs for Sky News.He asked how many children it is "legitimate and proportionate" to kill, including those being treated […]
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