The men were detained in the southern city of Granada after historic accusations were made.
The country's interior minister, Jorge Fernandez Diaz, said the arrests happened early on Monday and related to claims from ten years ago.
Last week the diocese suspended several priests following an intervention by the Pope.
It's reported the pontiff personally phoned the alleged victim to speak to him about his claims.
The Vatican has refused to comment on the reports though, saying it's not policy to discuss Francis' 'personal and pastoral' activities.