The fire started near Mount Hymettus, on the outskirts of the Greek capital, on Friday, leading to smoke spreading across the city.
Authorities say two men - a Greek and a Bulgarian - will be brought before a prosecutor.
Greek media reported that the men were beekeepers.
The men, aged 67 and 58, are accused of accidentally spreading a fire.
Tovima newspaper said the fire was started by tobacco, although it is not clear whether the men were smoking or using tobacco as smoker fuel for beehives - an occasional practice among bee-keepers.
The fire threatened homes in three different districts before being brought under control.
On Friday, more than 80 wildfires started in Greece, with the Peloponnese district particularly badly affected.
Greek media reported on Saturday that most of the fires were now under control.
Two men have been arrested for accidentally starting a fire that quickly spread on hills near Athens, the city's fire department says.