As Egypt braces itself for more possible clashes in the wake of this week's military coup, it's business as usual in the country's most popular holiday resorts.

While some tour operators have cancelled flights to Luxor and Cairo and rerouted cruises following Foreign Office (FCO) advice against all but essential travel to most of the country, travel to resorts on the Red Sea, including Sharm el-Sheikh, Taba, Nuweiba, Dahab and Marsa Alam remains unaffected.

Approximately 20,000 British holidaymakers are currently in the country, around 90% of whom will be staying in Red Sea resorts, according to the Association of British Travel Agents (Abta).

Britain's two biggest tour operators, Thomson and First Choice, currently have 9,000 clients in Egypt, 8,500 of whom are in Sharm el-Sheikh and "continuing to enjoy their holidays as normal".

In a statement released today the companies said: "The atmosphere is quiet and calm, with Sharm el-Sheikh's main resort of Naama Bay bustling. People should also take considerable reassurance from the fact that the resort of Sharm el-Sheikh operates like a country in itself. It is run separately from the rest of the Egypt, benefits from having just one secure road into the resort, and enjoys an exceptionally low crime rate."

Although the FCO is not advising British nationals to leave immediately, it said they should "consider whether they have a pressing need to remain." Thomson and First Choice cancelled all outbound flights to Luxor on 3 July, and repatriated all customers holidaying in Luxor back to the UK yesterday. There were no flights scheduled for 4 or 5 July.

A spokesman for Abta said holidaymakers who have had their holiday cut short - and who booked their holiday through a tour operator - could expect a refund on any unused hotel rooms or apartments, but independent travellers who are not on a package holiday are highly unlikely to receive any refund on unused accommodation, and will have to approach their airline directly if they want to fly back early, without paying a fee. British Airways is waiving its usual charge, allowing passengers to change the date of their flight or rebook to a different destination up to and including 10 July.

British travellers who are in the affected areas are being advised by the FCO to stay in or close to their hotel.

The latest unrest is a further blow to the Egypt's tourism industry which was only just starting to recover from the first Arab spring on visitor numbers, and was thrown into further disarray by the resignation of the tourism minister Hisham Zazou earlier this week.

But Abta said the effect on travel to the country would be relatively minor as it is not peak season, and is expected to be short-lived. "We are hoping that the situation will return to normal fairly quickly. The main concern for travel industry is that you have a stable situation."

In the meantime, tour operators are monitoring the situation. Peter Hilton, Middle East product manager at Cox & Kings which sells cultural and beach holidays, said it has no clients in the country at the moment. "The next clients due to travel there go at the end of next month. We've had a few calls, but these have been from people who are travelling much later in the year. If the advice stays as it is, then they won't be able to travel and we would refund them."