Lufthansa has resumed flights from Cairo, but British Airways says services will still be cancelled for another six days as a “precaution”.
On Saturday BA alerted passengers who were about to board a plane from Heathrow to the Egyptian capital.
German airline Lufthansa also stopped flights between Cairo and Frankfurt and Munich but they resumed on Sunday.
BA took the decision to suspend flights on the Heathrow to Cairo route for “security reasons”.
The British government said it was aware of BA “notifying passengers” of the decision to temporarily stop flights to Cairo.
The UK Foreign Office has updated its advice, saying “there is a heighted risk of terrorism against aviation”.
A BA spokesman said on Saturday: “We constantly review our security arrangements at all our airports around the world, and have suspended flights to Cairo for seven days as a precaution to allow for further assessment.
“The safety and security of our customers and crew is always our priority, and we would never operate an aircraft unless it was safe to do so.”
BA currently runs one flight from Heathrow to Cairo and back again per day – and says flights will continue to be suspended between the capital cities until next Saturday, 27 July.
Egyptair is continuing to fly twice daily between Heathrow and Cairo – and flights from UK airports to other parts of Egypt are still scheduled.
The Independent’s travel editor Simon Calder told the BBC: “It seems to be specifically British Airways and specifically Cairo to Heathrow which is the concern.”
A spokesman for Cairo airport told the BBC the airport had yet to be notified by BA of any such changes.
Christine Shelbourne, 70, from Surrey was due to go to Cairo for a week on Saturday with her 11-year-old grandson. She said she managed to check into the flight at 15:00 BST (14:00 GMT). However, her boarding card wouldn’t open the barriers.
“The check-in staff reissued my boarding pass and I tried again but that didn’t work either and we were told to try again in half an hour,” she said.
“Whether they knew anything I don’t know, but my husband told me the flight had been cancelled before they did. There were no suggestions or help from staff about alternative flights.”
“My 11-year-old grandson is heartbroken – he’s been looking forward to the trip for months. We’re just not going now,” she added.
“It was handled badly to be honest. My grandson is currently looking for flights for us – he’s devastated.”
One passenger named Dan said the airline had given customers £5 food vouchers “meant to last 24 hours”.
Michael Khalil, 42, from Guildford says he is about £1,200 out of pocket as a result of his flight being cancelled.
He was booked on the flight earlier on Saturday but ran to Terminal 2 and used his own money to book on to another flight.
Mr Khalil works in training and development. He says he has an important business meeting on Monday and told the BBC: “I have no choice. I have to be there.”
Safaa Almaghrabi was due to fly to Cairo on 24 July with her husband and six children for her sister’s wedding on 26 July.
The 31-year-old says she cannot find any direct flights. When there were some available earlier on Saturday, they were more than £35,000 for the whole family.
“We contacted British Airways and they had two nonsense solutions. The first was to book us a flight on the 31 July, the earliest flight they can. And this way we’ll miss the wedding,” she told the BBC.
They also offered her a full refund which she says is “really disappointing and unfair”.
The only indirect flights she can find are via Dubai, and Jordan which she said “will be horrible for six kids”.
She said: “I cannot afford to go but I have to go.”
Hannah Lilley, from London, was due to be flying to Cairo this Thursday for a “once-in-a-lifetime holiday”.
She told the BBC: “I am grateful for security and of course it is important to be safe.
“However, the communication from BA has been very poor. I am gutted at the damage to my summer.
“My holiday was booked in February. Flights with BA, a tour of the Nile from Cairo to Aswan across eight days and a couple of days at a resort by Giza.
“I have to wait until Monday to get through to my insurers to try and get all these different costs back.”
Current UK Foreign Office (FCO) advice on travel to Egypt warns against “all travel” to certain parts of the country.
But Cairo is part of a safer region where the FCO only suggests reviewing its advice before visiting.
Following the bomb explosion that destroyed a Russian airliner over Egypt’s Sinai peninsula in October 2015 after it had departed Sharm El Sheikh airport, the UK was one of a number of countries to temporarily suspend flights to and from the country.
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