Air fares are more than six times higher than normal for flights from Paris to London on Friday, with the cheapest British Airways tickets being sold for £452.
The lowest priced Eurostar tickets available on Friday morning are £210.
Travellers willing to pay these high fares could still miss out due to many services already being fully booked.
A British Airways spokesperson said the airline had not increased its ticket prices.
The company is allowing customers to bring forward their return trips at no extra cost, and using larger aircraft on affected routes.
In a statement on the six new countries removed from the travel exemptions list, BA said: “We are currently operating a limited schedule to these countries. As always, if a customer's flight is cancelled they are entitled to a voucher or a full refund.
"Our Booking with Confidence policy now covers customers due to travel up to the end of September 2020.
"It allows customers to book a trip now, with the confidence that they can change the date or destination and re-book their journey for travel until April 2022.
"This means that if a customer wants to change their booking they can – re-booking or taking a voucher for future travel.”
Transport Secretary Grant Shapps insisted the Government had taken “a practical approach” to the new restrictions.
It was announced on Thursday night that people arriving in the UK from France after 4am on Saturday will be required to spend 14 days in self-isolation due to rising numbers of coronavirus cases there.
The quarantine conditions will also apply to travellers returning from the Netherlands, Monaco, Malta, Turks & Caicos and Aruba.
Mr Shapps said an estimated 160,000 holidaymakers are expected to try to return to the UK from France on Friday.
There “had to be a cut-off”, he told BBC Breakfast.
“It’s a practical approach as well, which has enabled all fours parts of the United Kingdom – Scotland, Wales, Northern Ireland and England – to implement the same time at 4am where there are no flights in the air, at least tomorrow.”
He added: “You can always argue one way or the other. We have to make a decision on it and we have to do that based on science and medicine, and that’s what we’ve done, we’ve taken the advice and implemented on that basis.”
The move, which applies throughout the UK, comes after Boris Johnson promised to be “absolutely ruthless” in decisions about imposing new quarantine restrictions.
The Joint Biosecurity Centre and Public Health England detected a significant change in Covid-19 risk in all six destinations.
Department for Transport officials said data from France shows that over the past week there has been a 66% increase in newly reported Covid-19 cases and a 52% increase in the weekly incidence rate per 100,000 population, indicating a sharp rise in infections.
The latest 14-day cumulative figures from the European Centre for Disease Prevention and Control show 32.1 coronavirus cases per 100,000 people in France, compared with 18.5 in the UK.
The move will come as a bitter blow to the hard-pressed French tourism industry which relies heavily on visitors from the UK.
France’s secretary of state for European affairs said the UK decision would lead to “reciprocal measures” across the Channel.
Clement Beaune tweeted: “A British decision which we regret and which will lead to reciprocal measures, all in hoping for a return for normal as soon as possible.”
Speaking on BBC Radio Scotland on Friday morning, Humza Yousaf, Scotland’s cabinet secretary for justice, said: “These are very difficult decisions that we make.
“We make them based on the data we get in front of us and we received data from the French government yesterday evening and it’s very clear from the analysis that we had to act and act quickly.
“There is a period, a window, for them (travellers) to get back. But I’m afraid if they can’t get back before that, they will have to self-isolate for 14 days.
“There’s nothing additional that we will be able to do in terms of flights or by other ports of entry such as sea or rail – certainly nothing the Scottish Government can do.”
The decision to add the Netherlands was made after a 52% increase in newly reported cases between August 7 and 13 after a consistent series of rises in previous weeks.
Over the past week, there has been a 273% increase in newly reported cases in Turks & Caicos, a 1,106% increase in Aruba and a 105% rise in Malta.
A message from the Editor
Thank you for reading this story on our website. While I have your attention, I also have an important request to make of you.
The dramatic events of 2020 are having a major impact on many of our advertisers - and consequently the revenue we receive. We are now more reliant than ever on you taking out a digital subscription to support our journalism.
By supporting us, we are able to support you in providing trusted, fact-checked content for this website.