Those dead include the tourist vessel's captain and a nine-year-old girl, a coastguard spokeswoman said.
Three of the victims are Greek but the fourth, a man, has not been identified.
The motorboat's pilot was arrested, she added.
Five people were also hurt in the crash off Egina, an island near the capital where many Athenians have summer homes, officials said.
Among those injured is a 28-year-old woman who lost her lower leg in the accident, reports said.
"We saw over 8-9 people in the sea... Some were swimming, others were unconscious, dead," a witness told Greece's Mega broadcaster.
Another witness told Skai radio that the motorboat, which had four people on board, had sliced the launch in two as it sailed to a small islet off Egina popular with swimmers.
"I saw a little girl... Being given CPR but she was not responding," the second witness said.
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