The clouds brought dust from the Sahara desert, turning the Greek capital Athens orange.
According to officials, it is one of the worst such situations to hit Greece since 2018.
Similar clouds hung over Greece at the end of March and at the beginning of April, and they were also over parts of Switzerland and southern France.
The sky is expected to clear on Wednesday, the Greek Meteorological Service said.
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Air quality worsened in many parts of the country, and on Wednesday morning the ancient Acropolis in Athens was not visible due to dust.
The cloud reached as far as 500 kilometers north, to Thessaloniki.
People with respiratory problems were advised not to be outside much, to wear protective masks and to avoid physical exercise until the dust clouds cleared.
The Sahara releases 60 to 200 million tons of mineral sand per year.
Most of the sand quickly settles to the ground, but some of the small particles can travel far, sometimes even reaching Europe.
The atmosphere, especially in southern Greece, became suffocating due to the combination of sand and high temperatures.
Meteorologist Kostas Laguvardos compared the view from a meteorological station to the planet Mars.
On Tuesday, the fire department reported 25 fires in the last 24 hours.
One fire broke out near a naval base on the island of Crete, where temperatures above 30 degrees Celsius were measured, and some people were evacuated, according to local media reports.
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