Guidelines on the execution of England's new "red list" quarantine rules were reportedly only given to Border Force staff a few hours before they came into force.
As of Monday, travellers arriving in England were told to quarantine in a hotel if they have been in one of the Government's 33 "red list" countries in the past 10 days.
However Border Force sources told The Guardian immigration control staff received a lengthy email with five attachments, detailing official guidance for executing the new border checks, at 9.25pm on Sunday.
Under the new rules, immigration control staff must check each traveller's completed passenger locator form and hotel quarantine booking.
They must also verify passengers have received a negative Covid test, along with evidence of two additional test bookings for their 10-day quarantine period.
Sources told the paper a significant number of staff would not have seen the email by the time they began their shifts on Monday.
One Border Force staff member who was on duty at Heathrow Airport for the first day of the new border checks reportedly described the process as "an absolute joke".
A spokesman for the PCS union, which represents Border Force staff, told the paper: "It is a disgrace our members in Border Force only received new guidelines on hotel quarantine late last night.
"It's vital that Border Force are equipped to deal with helping the public stay Covid safe. However, many feel underprepared and under valued by a department that is not doing its job."
The email, sent by senior Home Office staff, reportedly said the new process "will be a lot to absorb" and admits there will be "bumps along the way".
The Home Office has been approached for comment.
Meanwhile a father and daughter who went into hotel quarantine in Scotland on Monday were allowed to leave after a day due to a loophole with their arrival.
All passengers arriving in Scotland on international flights have to enter "managed isolation", unless they are coming from within the Common Travel Area, which includes the UK and Ireland.
Chun Wong told BBC Scotland he and his daughter flew into the country from the United States via Dublin, and went straight to a hotel at Edinburgh Airport.
Mr Wong told the broadcaster: "I received a call from reception saying a gentleman from the airport would like to talk to me.
"He said that since I landed in Dublin first and then got a connecting flight to here, I was not required to quarantine in a hotel.
"I still have to quarantine and do the self-testing kit on the second and eighth day, but they said it was an error on their part."
Scottish First Minister Nicola Sturgeon has expressed concern about gaps in the current system for international arrivals, telling a coronavirus briefing in Edinburgh on Monday: "It would be better if we had that four nations approach, or at least a three nations approach where the border of the island that Scotland, England and Wales share, had the same provisions in place."