A mattress had been placed underneath the bus in the early hours of Thursday and set alight, it said.
"Our team bus has been completely damaged in a cowardly arson attack over night. No one was injured. Police have arrested a suspect," said a statement on the team's Twitter account, showing images of the burned vehicle.
The team were competing in their first Grand Tour.
They have vowed to continue racing and posted a picture of their riders on a different bus on their way to stage 12, which begins in Motril later on Thursday, with the message: "Nothing is going to stop us starting today's La Vuelta stage. Thank you for all the support."
— Aqua Blue Sport (@AquaBlueSport) August 31, 2017
A statement from Spain's national police force said they had arrested a 55-year-old man who had allegedly caused four fires in Almeria, in the province of Andalusia.