Hundreds of sunbathers were on the popular beach at Caparica, 30 kilometers (20 miles) south of Lisbon, and witnesses said some sunbathers ran into the sea to avoid the plane.
The National Maritime Authority said the man and girl died on the beach. Officials said they were not aware of any injured.
The small aircraft, reportedly a Cessna, carrying two people appeared to be in difficulty and wobbled as it skimmed low over the sunbathers, scattering them and spreading panic on the beach, witnesses said.
The plane appeared to have a partly broken left wing, which hung lower than the right wing, Portuguese television pictures showed. Officials said the accident occurred at 4:50 p.m. (1550 GMT).
The dead girl was with her parents, who were unhurt, witnesses told local television channels. The plane passed over the dead man's legs as he sunbathed on a towel, they said. No others were reportedly hurt.
The bodies lay covered on the sand as police cordoned off the area.
The two occupants of the plane were unhurt and were being questioned by police.
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