British Airways has suspended flights to Cairo for seven days amid security concerns.
Some passengers at Heathrow Airport were told after they travelled there to board their flights on Saturday.
A letter handed to travellers and later posted on social media said the decision was made "as a precaution" following a review of "security arrangements".
The latest Foreign and Commonwealth Office (FCO) guidance states there is a "heightened risk of terrorism" against flights from the UK to Egypt and says here are already "additional security measures are in place".
It adds: "Terrorists are very likely to try to carry out attacks in Egypt. Although most attacks occur in North Sinai, there is a risk of terrorist attacks across the country."
The FCO advises against travel to much of the country, but popular tourist areas such as Hurghada, Abu Simbel and Luxor are considered safe.
Three Egyptian airport security sources told Reuters that British staff were checking security at Cairo airport on Wednesday and Thursday.
Egypt's tourist industry has declined in recent years following a spate of terror-related incidents.
More than 1.5 million British visitors travelled to the country in 2010, but the number had fallen to 415,000 last year, according to the Foreign and Commonwealth Office (FCO).
BA and Egypt Air are the only two airlines that run flights from Heathrow to Cairo.
BA said in a statement: "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."
A spokeswoman later added: "We are rebooking customers who wish to travel this week on flights with alternative airlines. Customers who no longer wish to travel will be offered a refund."
It is understood British Airways made the Department for Transport aware of its decision ahead of the announcement.
German airline Lufthansa has also suspended flights to Cairo but says it plans to resume them on Sunday.