Authorities said the incident took place on Sao Joao beach in Caparica, south-west of Lisbon.
The National Maritime Authority said a middle-aged man and a young girl died after they were unable to avoid the plane.
The plane's only two occupants were unharmed, it added.
The Diario de Noticias newspaper quoted an eyewitness who said the plane had been flying at a low altitude over the beach, although he did not realise anything was wrong until other beachgoers began running.
One young witness told Reuters news agency: "I was near the water when I saw the plane. I called my parents, the plane fell on the sand and ran over two people, fatally hurting them and another was injured, I think, but I'm not sure, people were running away.
"The plane is still there, but the ambulances arrived quickly. I think maybe the fuel ran out because I find it weird that it landed on the beach."
Other reports said the victims had been sunbathing when the plane made its emergency landing.
The Associated Press news agency said the girl who died had been with her parents, who were unhurt. The agency quoted witnesses from local television broadcasts.
Joao Quadros, who was on the beach, tweeted photos of the aftermath, saying the plane had passed by his son by a matter of metres. There had been no noise, he said.
The National Maritime Authority said a middle-aged man and a young girl died after they were unable to avoid the plane.
The plane's only two occupants were unharmed, it added.
The Diario de Noticias newspaper quoted an eyewitness who said the plane had been flying at a low altitude over the beach, although he did not realise anything was wrong until other beachgoers began running.
One young witness told Reuters news agency: "I was near the water when I saw the plane. I called my parents, the plane fell on the sand and ran over two people, fatally hurting them and another was injured, I think, but I'm not sure, people were running away.
"The plane is still there, but the ambulances arrived quickly. I think maybe the fuel ran out because I find it weird that it landed on the beach."
Other reports said the victims had been sunbathing when the plane made its emergency landing.
The Associated Press news agency said the girl who died had been with her parents, who were unhurt. The agency quoted witnesses from local television broadcasts.
Joao Quadros, who was on the beach, tweeted photos of the aftermath, saying the plane had passed by his son by a matter of metres. There had been no noise, he said.
