The three children, aged three, five and seven, are currently living in a childrens' home in the town of La Carolina in the southern province of Jáen.
Their father, 47, picked them up on Tuesday, June 2nd but never returned them, reporting at around 6.30pm that his children had "disappeared" while they were in a park close to the centre of the town.
Spain's Civil Guard police immediately launched a huntfor the three siblings that included searching vehicles on the local motorway and issuing a nation-wide alert.
Police officers have confirmed to Spanish daily, 20 minutos, that the children were in care and that the father "wanted to take them"; their disappearance raising suspicions that their father kidnapped them with the help of a third party.
The father was arrested at 10.50pm on Tuesday as the presumed mastermind behind the kidnapping of his three children.
Justice minister in Andalusia's regional government, Emilio de Llera, told 20 minutos that authorities hoped to soon find the three children and that "nothing bad has happened to them".
"It's something that can happen," he said, adding that "parents can sometimes lose their children".
Andalusia's regional government has opened an investigation into the whereabouts of the children.
When asked if the father was supervised during the visit, Purificación Gálvez, a representative of Andalusia's government said the issue was "very complicated issue of red tape" and refused to elaborate further.