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 FCO guidance states there is a "heightened risk of terrorism" against flights from the UK to Egypt and says there are already "additional security measures are in place".
They advise against travel to much of the country, but popular tourist areas such as Hurghada, Abu Simbel and Luxor are considered safe.
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."