Seven successive tremors measuring over 4.0 magnitude were recorded in the early morning by the Athens Geodynamic Institute, Greece's leading authority on earthquake analysis.
This was after a 5.2 quake, the strongest so far since the weekend, was recorded on Wednesday evening.
Experts have so far been unable to give a definitive estimate on when the seismic activity will end, but stress that it is unprecedented.
"The intensity is falling but has not yet stabilised," the institute's research director Athanassios Ganas told state TV channel ERT.
"We're at the halfway point," the institute's deputy director Vassilis Karastathis told the station.
The institute on Thursday said over 6,000 tremors had been recorded in the area near the islands of Santorini, Amorgos, Anafi and Ios since January 26.
Over 11,000 residents and seasonal workers have left Santorini since the weekend by sea and air, with operators adding extra flights and ferries.
Experts say the region has not experienced seismic activity on this scale since records began in 1964.
Santorini lies atop a volcano which last erupted in 1950 -- but an experts' committee on Monday said the current tremors were "not linked to volcanic activity".
No injuries or damage have been reported.
But rescue teams have been sent to the area as a precaution, and additional seismic sensors have been deployed.
The head of Greece's earthquake planning and protection authority, Efthymios Lekkas, on Wednesday warned there were five areas at risk of possible rockslides on Santorini, including the ports of Fira and Athinios.
Schools on more than a dozen islands in the Cyclades have been shut as a precaution until Friday, prompting many people with children to leave Santorini until the quake scare eases.
Santorini attracted about 3.4 million visitors in 2023. Upwards of a million of those were cruise ship passengers.
European travel agents contacted by AFP said the number of foreign visitors to Santorini at this time of year was minimal, with more bookings expected in the spring.
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