A scientific committee monitoring the quakes gave the go-ahead last week, noting a fall in tremor intensity and the resilience of local public buildings.
"Based on inspections to this point, public buildings have responded well to the seismic load," the committee said in a statement.
Thousands of earthquakes, mainly of a low magnitude, were recorded from late January between the islands of Santorini, Amorgos, Ios and Anafi in the Cyclades group southeast of the Greek mainland.
The strongest tremors were between 5.0 and 5.3 magnitude.
They did not cause either casualties or significant damage but have worried authorities and residents.
The latest data shows tremors of under 4.0 magnitude.
The ministry attributed the recent activity to a combination of tectonic movement and deep magmatic activity.
The region has not experienced a phenomenon of such magnitude since records began in 1964, experts say.
Located where the African and Anatolian tectonic plates converge, the Aegean Sea is often hit by earthquakes.
Known for its spectacular volcanic crater or caldera, Santorini is also part of a volcanic arc with two underwater volcanoes near to its coast, Nea Kameni and Kolumbo, which last erupted in 1950 and 1650 respectively.
The ministry said preventative measures would remain in force and urged residents to be alert to the risk of landslides.
Authorities declared a state of emergency in Santorini and Amorgos at the start of February for a month.
Schools were closed and a majority of Santorini residents elected to leave the popular tourist destination, which saw 3.4 million visitors in 2023.
Prime Minister Kyriakos Mitsotakis recently announced a support package for local businesses and workers on the island.
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