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The trainee pilot and flight instructor of a small plane that killed two people while landing on a Portuguese beach have appeared in court.

The plane struck a 56-year-old man and an eight-year-old girl as it made an emergency landing on Wednesday.

Authorities said the plane suffered mechanical trouble as it flew above São João da Caparica beach, near Lisbon.

Reports said the two men in the plane could face a charge of negligent homicide and up to 16 years in jail.

They appeared at a preliminary hearing before a prosecutor near the Portuguese capital on Thursday morning.

The Diário de Notícias 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.

"The plane first hit the man, who had his back to it. Immediately after it lifted up and when it descended again it hit the child's head," another witness, Filipe Janeira, 34, told the Jornal de Notícias.

Agence France-Presse news agency said beachgoers surrounded the plane when it landed and confronted the two men inside.

"The girl's father and other people went to the plane and started hitting the rear," witness Celia Rocha told the Correio da Manhã newspaper .

The newspaper said that pilots were advised to veer away from people in an emergency, and to land in the sea instead of on a busy beach.

In August 2015, another small plane landed in the sea near the same beach after an engine malfunction.