The incident happened off the southern coast of the Gaza Strip within Palestinian territorial waters, Nizar Ayyash, spokesman for the union of Gaza fishermen, told the Palestinian Ma'an News Agency.
After the shots were fired, the fishing boat sailed away from the Egyptian vessel, Ayyash said.
Relations between Gaza and Egypt have been strained since the ouster of Egyptian President Mohamed Morsi in July.
In August, an Egyptian forces fired at Gaza fishermen, injuring two people and arresting six others.
2014: The Year in Music [PHOTOS]