The Belgian was apparently taking a drink from his bidon when he hit a hole in the road and crashed hard.
The 28-year-old was taken to hospital in Murcia with severe facial trauma and fractures, a concussion, broken ribs and a punctured lung. He is expected to be kept in the coma for a few days.
The incident affected his teammates deeply. "I didn't want to leave boeckie behind before i saw him awake. I was crying like a child seeing him on the ground like this," his teammate Thomas De Gendt said on Twitter.
Boeckmans' crash set off a chain-reaction that also involved Tejay van Garderen (BMC), Daniel Martin (Cannondale-Garmin) and Nacer Bouhanni (Cofidis) all of whom abandoned the race.