The Dutchman, who was at the race as co-leader of Jumbo-Visma, suffered a knee injury after he was involved in the team's crash during Saturday's opening team time trial.
The team announced via Twitter that the pain has escalated since then, leading to Kruijwsijk being forced out of the race on Tuesday.
Much of the squad was wiped out on stage 1, with four riders – including Primož Roglič – hitting the deck in Torrevieja. The crash was caused by a wet patch that had materialised on the road, supposedly caused by a burst children's paddling pool nearby.
A day later, Kruijswijk was among the GC men to shed time on the road to Calpe. He finished 1:43 down on stage winner Nairo Quintana, and lay 51st overall, 2:19 down on race leader Nicolas Roche (Team Sunweb) at the time of his abandon.