A suspect has been arrested after the incident in the southern Spanish city of Almeria.
"Our team bus has been completely damaged in a cowardly arson attack over night," Aqua Blue posted on their Twitter account, alongside a series of pictures of the damaged vehicle.
"No one was injured. Police have arrested a suspect."
Aqua Blue were still to take their place in Thursday's 12th stage from Motril to Antequera.
"Nothing is going to stop us starting today's La Vuelta stage. Thank you for all the support," the team added on Twitter.