Travellers from countries on the banned list can only arrive into one of five airports in England when new rules come in next week.
UK nationals or residents returning from 33 “red list” countries will be required to spend 10 days in a Government-designated hotel from Monday.
Guidance for those who have to quarantine in hotels was published on Thursday and states that anyone with a booking that brings them to a different “port of entry” from February 15 must change it to one of those specified.
The accepted entry points are: Heathrow Airport, Gatwick Airport, London City Airport, Birmingham Airport and Farnborough Airfield.
The guidance states that leaving the room for exercise will only be allowed with special permission from hotel staff or security and is “not guaranteed”.
The online portal for people coming in to the country to book a quarantine hotel has also gone live, but the site went down shortly after its launch.
On the Government website it stated that “due to a minor technical issue, the link to the booking portal in this guidance will not be available until later today”.
Many test bookings conducted by the PA news agency for a variety of airports and dates resulted in a message stating “we cannot find any applicable hotels”.
Shadow home secretary Nick Thomas-Symonds said ministers must act urgently to get it back up and running.
“It is extremely worrying that even the limited hotel quarantine booking system is showing signs of failing from the outset,” the Labour MP said.
“Over a year into this pandemic and 50 days on from the discovery of the South African strain, there are no excuses for yet more Government incompetence in the introduction of hotel quarantine.”
Health Secretary Matt Hancock announced on Tuesday that arriving travellers put in quarantine hotels will be charged £1,750 for their stay.
The guidance states that it will cost £650 for a second adult or child aged over 12 to stay in the room, and a further £325 for a child aged between five and 12.
The costs – which the Department of Health said will be reviewed before the end of March and may change – cover transport to the hotel, food, accommodation, security, other essential services and testing.
People on income-related benefits have the option to apply for a deferred repayment plan when booking, which will require them to pay back the cost in 12 monthly instalments.
Passengers arriving into England face fines of up to £10,000 for failing to quarantine, and those who lie on their passenger locator forms face up to 10 years in jail.
The Government guidance states that other ports of entry “may be added in the future” but for now anyone required to quarantine in a hotel who does not arrive at one of the designated airports “may face a penalty of up to £10,000 and will be charged for the cost of transportation” to the nearest designated entry point.
Mr Hancock told the Commons earlier this week that 16 hotels had been contracted to provide 4,600 rooms for the quarantine programme.
Travellers must take a Covid-19 test and have a negative result in the three days before travelling, and the quarantine package includes tests on the second and eighth day of hotel quarantine – except for children under five.
Anyone who has not booked their hotel quarantine before arriving in England faces a penalty of up to £4,000 plus the costs of their quarantine.
People can leave quarantine after getting a negative result on their day eight test and having quarantined for 10 full days.
Rory Boland, Editor of Which? Travel, said the Government must ensure there are enough hotel rooms available.
He said: “If mandatory hotel quarantine is to be effective, it is essential the Government ensures there is enough provision of rooms to accommodate UK arrivals from red-list countries, to save anyone being left stranded abroad and significantly out of pocket for reasons beyond their control.”
There are some exemptions to the mandatory hotel quarantine including Government contractors, defence personnel and hauliers travelling from Portugal.
The Scottish Government this week unveiled plans that will see every person arriving from overseas, rather than from specific countries, subject to a 10-day hotel quarantine.
Six hotels, near to Aberdeen, Edinburgh and Glasgow airports, have been block-booked to house travellers quarantining – with a combined total of up to 1,300 rooms available.