Local mayor Thymios Kotzias told media two masked men had broken into the museum after overpowering the sole guard, a woman.
Thymios Kotzias said items of “incalculable” value had been stolen, but gave no details.
Culture Minister Pavlos Geroulanos has tendered his resignation, state television reported.
Ancient Olympia, in Western Greece, is regarded as one of the most important cultural sites in the country.
Thymios Kotzias was quoted by AFP as saying: “There were two of them, and they had a gun.
“They immobilized the guard as the shift changed at 7:00 a.m., having previously knocked out the alarm.”
“We must wait and see what the local archaeology supervisor will say, but the items were of incalculable value,” Thymios Kotzias added.
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