A ministry statement said experts from Greece and the U.S. have found rough axes and other tools thought to be between 130,000 and 700,000 years old close to shelters on the island's south coast.
Crete has been separated from the mainland for about five million years, so whoever made the tools must have traveled there by sea (a distance of at least 40 miles). That would upset the current view that human ancestors migrated to Europe from Africa by land alone.
"The results of the survey not only provide evidence of sea voyages in the Mediterranean tens of thousands of years earlier than we were aware of so far, but also change our understanding of early hominids' cognitive abilities," the ministry statement said.
The previous earliest evidence of open-sea travel in Greece dates back 11,000 years (worldwide, about 60,000 years - although considerably earlier dates have been proposed).
The tools were found during a survey of caves and rock shelters near the village of Plakias by archaeologists from the American School of Classical Studies at Athens and the Culture Ministry.
Such rough stone implements are associated with Heidelberg Man and Homo Erectus, extinct precursors of the modern human race, which evolved from Africa about 200,000 years ago.
"Up to now we had no proof of Early Stone Age presence on Crete," said senior ministry archaeologist Maria Vlazaki, who was not involved in the survey. She said it was unclear where the hominids had sailed from, or whether the settlements were permanent.
"They may have come from Africa or from the east," she said. "Future study should help."
The team of archaeologists has applied for permission to conduct a more thorough excavation of the area, which Greek authorities are expected to approve later this year.