The epicentre of the magnitude 6 quake was 13 km west of Lefkada in the Ionian Sea, the Athens Geodynamic Institute said.
Police said a 59-year-old woman had been killed when her house collapsed after being struck by a falling rock in the seaside village of Ponti.
A local resident said a second woman had been crushed to death in a stable in the mountain village of Athani. Police could not confirm her death.
"There is a dead woman, the stable fell over her and we are still trying to recover her body under the rubble," Nikos Rombotis, 61, owner of a gift shop in the village, told Reuters by phone.
The quake also damaged the main road in the southwestern part of the island.
The U.S. Geological Survey registered the quake as magnitude 6.5.
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