Police are now questioning Ashya King's parents, Brett King, 51, and Naghemeh King, 45, who are Jehovah's Witnesses.
The couple took Ashya from Southampton General Hospital on Thursday afternoon before travelling to France. They were spotted in Spain on Friday before being traced by the authorities last night.
A member of the public is believed to have told Spanish authorities he had seen a child resembling the missing youngster travelling in a grey van in the Basque Country.
An arrest warrant had earlier been issued for the boy's parents, with Hampshire Police assistant chief constable Chris Shead saying the warrant related to "neglect".
However, the police chief added: "That does not necessarily mean they would be charged with that offence."
Fears had also been raised about the battery on Ashya's medical feeding system which was believed to be out of power. Officers appealed to the couple not to attempt to administer food themselves as his feeding and associated medical needs are "complex".