Travellers arriving in England from seven Greek islands will have to self-isolate for 14 days from 04:00 BST on Wednesday, Grant Shapps has said.
The islands affected are Crete, Lesvos, Mykonos, Santorini, Serifos, Tinos, and Zakynthos (also known as Zante).
The government says islands can be treated differently from their mainland countries if infection rates differ.
But airlines have been critical of the time it has taken – Easyjet’s boss said the change was “too little, too late”.
Speaking to MPs in the Commons, Transport Secretary Mr Shapps said the government would use better data to pinpoint risks on popular islands.
He said that would provide “increased flexibility” to add or remove them from the quarantine list for England – distinct from mainland destinations – as infection rates change.
He said this would “help boost” the UK’s travel industry while continuing to keeping the travelling public safe.
Mr Shapps said the coronavirus infection rate was still too high in Spain’s Balearic and Canary Islands to remove them from the list of destinations from where travellers returning to England must quarantine.
He said the government was “working actively on the practicalities” of using coronavirus testing to cut the 14-day quarantine period for people arriving in the UK from high-risk countries.
Purely testing people on arrival “would not work”, Mr Shapps said, but quarantine combined with testing was “more promising.”
“My officials are now working with health experts with the aim of cutting the quarantine period without adding to infection risk or infringing our overall NHS test capacity,” he said.
He added that if someone was unable to quarantine for 14 days after returning to the UK “it might be best not to travel”.
Devolved governments set their own travel rules and there are variations across the UK nations on some countries, including Greece.
Travellers arriving in Wales from six Greek islands must already quarantine – these islands are Crete, Lesvos, Mykonos, Paros and Antiparos and Zakynthos.
For months, the UK government has been lukewarm about the idea of only applying travel quarantine on a regional basis.
Last week it came under sustained pressure from bosses in the aviation sector.
They’re desperate to know when international travel might recover in a meaningful way.
One airport boss was scathing, accusing the government of “overseeing the demise of UK aviation”.
The Welsh government also then decided its travel quarantine would, in the case of Greece, be managed on a regional level, with six Greek islands added to its list.
The UK government says its decision to regionalise quarantine now for England is driven by improved availability of data at a regional level in countries abroad.
But the change isn’t silencing the critics.
Easyjet is the latest big name in travel to lay into the government. Its boss told me the situation is too confusing and much of the damage has already been done.
His warning to ministers: come-up with a substantial recovery plan for UK aviation or much of the damage to the sector will be permanent.
Labour’s shadow transport secretary Jim McMahon described the government’s handling of the pandemic as “chaotic”, saying that “for months” there had been no restrictions on travellers entering the UK.
“By the time restrictions were introduced, we were one of only a handful of countries in the world who had failed to take action,” he said.
Johan Lundgren, the boss of airline Easyjet, told the BBC the government’s latest change to its quarantine rules was “too little, too late”, as the peak of the summer holiday season had passed.
“This is something we have argued for a long time – it should not have been a blanket instrument when it comes to quarantine. It should be based on risk and on a much more targeted approach,” he said.
He urged the government to devise a plan for UK aviation, warning that the sector would not recover in a meaningful way without one.
A spokesman for British Airways’ owner IAG said it was “evident” in July that islands should be treated separately and the government was “too slow in making obvious decisions”.
“For most families, summer is now over and the damage to the industry and the economy is done,” he said.
“We need to get on with (testing). We are way behind other countries on what has to be a more nuanced approach.”
Airport Operators Association chief executive Karen Dee welcomed the change in approach but said it was unlikely to significantly improve consumer confidence, while quarantine was “devastating the UK aviation industry”.
Tim Alderslade, chief executive of Airlines UK, which represents UK carriers, said a testing regime was “urgently required”.
Heathrow Airport welcomed the announcement that testing to shorten quarantine was being considered by the government and that air bridges to islands would be used where appropriate.
“If introduced, these vital policy changes would show the government understands how critical the restoration of air travel is to this country’s economic recovery,” a statement said.