The team posted photos on social media showing the rear of the bus was gutted by the fire in Almeria.
Aqua Blue Sport wrote on Twitter: “Our team bus has been completely damaged in a cowardly arson attack over night. No one was injured. Police have arrested a suspect.”
Aqua Blue Sport were staying at the Tryp Indalo Hotel in Almeria overnight and the bus was parked outside.
Cycling teams use their buses as their base for riders to change and to hold team meetings, as well as transport.
The Cork-registered team are making their Grand Tour debut in the Tour of Spain and remain committed to the race.
Race organisers have provided Aqua Blue Sport with a 52-seater coach for use on Thursday’s 12th stage from Motril to Antequera Los Dolmenes. The race finishes in Madrid on September 10.