Brittany Ferries, which is the primary ferry operator at the port, has seen 35,000 of its passengers either cancel or move their reservations over the weekend – with many changing their reservations to next year.
The ferry firm, which is also runs services from Plymouth, runs 80 per cent of its passengers through Portsmouth.
On Thursday, the government announced that anyone arriving from France after 4am on Saturday will need to quarantine for 14 days.
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Around half of those booked to travel to France this weekend cancelled their plans, according to a spokesman from Brittany Ferries.
He said: ‘Over the weekend around 35,000 passengers booked with us in the immediate future either cancelled or moved their reservations.
‘The good news is that many of those moved to next year.
‘In terms of those travelling to France this weekend, around half of those who were originally booked travelled.’
Even though the company experienced more booking movements than cancellations, the ferry firm was in for a ‘very tough autumn and winter’, according to the spokesman.
He added: ‘Unfortunately, weak forward demand for autumn means we may have to make some tough decisions about which services we run and which we don’t in the months to come.
‘That is the reality of our difficult decisions, but we apologise in advance for any inconvenience to passengers.
‘So, as long as we can get through what is going to be a very tough autumn and winter, we should be able to make up ground again in 2021.’
The ferry firm is currently lobbying the French government to scrap plans that would impose a reciprocal quarantine measure on arrivals from the UK.