Boris Johnson has banned foreign nationals from 33 countries, including all of South America, southern Africa, Portugal and the United Arab Emirates.
It comes after it emerged travellers from the 33 "red list" countries were not kept separate from other passengers, raising fears of spreading mutant strains of the virus.
According to The Times, no routine protocols have been put in place to limit interaction before travellers are identified and forced to self-isolate in hotels.
Gavin Newlands MP, the SNP's shadow transport spokesperson, has now urged the Prime Minister to rethink the scheme.
He said: "Reports that in England travellers from 'red list' countries may be able to mix with other passengers in the airport before going into hotel quarantine are concerning and risk undermining efforts in tackling and suppressing the virus.
"In Scotland, the Scottish Government has introduced managed quarantine for all arrivals into the country.
“The move has been driven by the best scientific and public health advice and on lessons learned from our experience with the virus.
"The Scientific Advisory Group for Emergencies (Sage) has already said that 'geographically targeted travel bans' were not enough to stop new coronavirus strains from arriving in the country, and the only way to 'get close' to stopping them was to close the borders completely or introduce mandatory hotel quarantine measures for everyone entering the UK.
"Even at this late stage, the UK Government must rethink its approach and follow the lead of the Scottish Government in strengthening measures for those arriving into the country.”
Scotland is requiring hotel quarantine for all international arrivals, with England just telling those from non-red list countries to quarantine at home for ten days.
An aviation industry source said: "From a public health perspective, if these people are indeed dangerous and at risk of spreading variants, then it doesn't make much sense to let them freely mingle.
“Perversely, the cancelling of direct flights has made this whole thing much more complicated."
It comes as Heathrow, Britain’s busiest airport, warned recent queues at passport control have been up to five hours.