The Government has reintroduced the need to book a quarantine for travellers coming back to the UK from red list countries. There are currently 11 countries on the red list.
It was revealed parents were forced to quarantine up to 100 miles away from their children due to the lack of space.
One family from Sheffield was split into two rooms.
They were told they could not stay in one double room and had to pay for two rooms, one for the mother and one for the father and their six-year-old son.
One room is in London Gatwick, while the other is in Milton Keynes.
This came at a cost of more than £4,500 to be allowed to come home from South Africa.
Their MP, Olivia Blake, said the situation was “ridiculous”.
She also said she knew of other similar cases.
She tweeted: “My constituent is having to quarantine 100s of miles from her young son and partner, in a separate hotel room, because of the huge shortage of family sized quarantine rooms.
“I’ve written to Sajid Javid to demand urgent steps are taken to ensure family rooms are made available.”
The boy’s grandmother, Janine Akers, said: “They haven’t told their son yet and I don’t know what the stress is going to be when he’s told.
“When they got the two room bookings confirmed they had no choice but to take them otherwise they may have been stranded over Christmas.”
The costs are adding up for the family, with the Janine saying they were now £6,000 out of pocket.
On top of the two quarantine hotel rooms, the family had to find additional accommodation in South Africa, and they had to defer their flights.
A spokesperson for the Government said: “The quarantine measures we have in place are minimising the risk of variants coming into the UK and safeguarding the hard-won progress of our vaccination programme.
“The majority of passengers who have used the Managed Quarantine Service have been satisfied with the service and we aim to keep families together. We would advise guests to raise any concerns with hotel staff in the first instance.”
It is understood families placed in separate rooms will not be allowed to interact, unless there was an interconnecting door between the rooms and they were from the same family.