The attack came at the end of a day of clashes with Israeli troops along the land border with Gaza, in which three Palestinians were killed and Israel said there was a mass attempt to break through the frontier fence into the Jewish state.
The Israeli military said in a statement that its warplanes "targeted six military targets belong to the Hamas terror organisation's naval force in the Gaza Strip."
It did not give the location of the targets.
Eyewitnesses at the port said the two boats were badly damaged.
Hamas security forces prevented journalists from reaching the scene.
It is believed to have been the first time Israeli aircraft had targeted boats in Gaza since the 2014 war there between Israel and Hamas.
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