The holiday island has been hit hard by severe flooding stranding hundreds of holidaymakers.
Torrential rains have turned roads into rivers, cutting off some areas.
The Foreign Office updated its travel advice for Greece with an extreme weather warning.
Cars were washed away in fast-moving storm waters and holidaymakers have been evacuated.
“We are continuing to closely monitor the weather conditions,” Jet2 said.
“We believe (cancelling) is the right thing to do in terms of allowing the island and its population to quickly return to normal.”
“We will be contacting affected customers with regards to their refund and rebooking options.”
Jet2 said it will fly empty to Skiathos to bring customers back to the UK.
“We will review this closely and may put on additional aircraft to fly customers home if required.”
“Our absolute focus is on doing everything we can to look after everyone.”
Some holidaymakers reportedly remain trapped on upper floors of hotels without power and running water.
At least two people have died and several are unaccounted for.
Greek authorities said the rains from Storm Daniel were the heaviest since records began
Greek Prime Minister Kyriakos Mitsotakis cited climate change as a factor for the floods as well as the recent wildfires.
“I am afraid that the carefree summers, as we knew them… will cease to exist.”
In some parts of Greece, a year’s worth of rain fell in a single day.
Tags: Skiathos flights, Jet2
