Fully-vaccinated travellers faced queue chaos at Heathrow airport after E-gates failed to recognise their status.
The E-gates only allowed holidaymakers from green list countries and travellers who had to quarantine at home to pass unhindered.
Vaccinated travellers from amber list countries, however, were blocked and forced to queue for paper checks on their documents by Border Force officers.
One double jabbed passenger returning from Faro in Portugal on Monday told how he had to queue for 90 minutes after being rejected by the E-gates, which should have allowed him through in 90 seconds.
He said the problems were compounded because only two of a possible five Border Force officers were on duty, leaving three desks unstaffed.
“It seems as though anyone arriving from a Green country, and anyone who has declared they will self isolate and do their day 2 and day 8 PCR test, can get through the E-gates,” he said.
“But passengers arriving from amber countries who from today are exempt from self isolation cannot use the E-gates. It could be that the technology has not been updated to take account of the new rules governing arrivals from amber countries.”
Travel countries on the red, green and amber list
Industry officials suggested the problem stemmed not from the technology but the way the passenger locator form had been rewritten to include a traveller’s vaccinated status.
They said this had led to confusion over whether they were travellers exempted from quarantine by their profession or allowed not to self isolate because of their vaccination status.
Officials said the form had been restructured to avoid the confusion but there were still concerns that there could still be delays over the next 48 hours.
The hotel quarantine 'red list' countries
A Government spokesman said: ““Our utmost priority is protecting the safety and health of the public. That means, occasionally, passengers will need to accept an increase in the time taken to cross the border.
“We are aware that a number of passengers arriving from amber list countries encountered difficulties passing through E-gates as the option they selected meant they needed to be assessed by an officer rather than use E-gates.
“We have now updated our form so it is clearer for those who do not need to quarantine and we continue to review and modify our approach to ensure full compliance with border and biosecurity checks.”