Three people have been charged by police over the disappearance of a 10-year-old Adelaide boy in an apparent hoax.

The 10-year-old, who went missing from his father's boat in Port Adelaide on Tuesday, was located safe and well at a house in the Adelaide suburb of Sturt, about 5pm (CST) on Friday, police said.

His disappearance had sparked a massive search involving police, about 30 State Emergency Service volunteers and a helicopter.

Police divers twice searched the river where the boat was moored, Superintendent Anthony Fioravanti told AAP.

He said a 42-year-old female at the house where the boy was found had been arrested and charged with hindering police.

A 43-year-old man of Aldinga Beach has been arrested and charged with impeding an investigation.

A 49-year-old man has been arrested and charged with creating a false belief, Supt Fioravanti said.

All three will appear before Port Adelaide Magistrate's Court on Monday.

Police investigations are continuing, but it is believed that the boy's disappearance was linked to a pending custody dispute between his estranged parents.

Police are likely to pursue compensation for the costly search, which appears to have been the result of a hoax.

"It's highly probable that we will be making an application for compensation," Supt Fioravanti said, adding the claim would be in the "tens of thousands of dollars".

Supt Fioravanti said the boy was in good spirits when he was found by police at the house.

"It would appear that he was there of his own free will and he knew that person he was staying with," Supt Fioravanti said.