Instead the team has a youthful line-up, while Rujano, third in the 2005 Giro, will switch focus to racing later in the summer.
"We concluded there was no facts against him, since the suspect blood values could not be used against him," said Dutch team manager Daan Luijkx, "The products Rujano was involved with don't figure on the banned list. If we stick to the rules he could run. But we prefer not to take the risk.
"We do not want to risk discrediting the organisers, team, sport, and the rider himself while he is the subject of an investigation."
Sport director Jean-Paul van Poppel added: "The facts on Rujano in the Italian investigation seem pretty innocent but to get a credible sport we cannot take decisions on the fact that it seems innocent.
"We have to put to light on orange for him as long as the public prosecutor doesn’t take a decision and this decision will be taken in May according to Italian insiders.
"Lammertink and Wauters debut in a giant tour and it will be a trip in which they can explore their boundaries. Both riders are fit and prepared after the first month of the season. The fact that they are solid in the mountains gives me the confidence that they will be able to finish the race.
"I expect that we will see them, like the others on the team, in the picture a few times."
Full Vacansoleil roster for the Giro d'Italia: Grega Bole, Martijn Keizer, Maurits Lammertink, Pim Ligthart, Marco Marcato, Rob Ruijgh, Willem Wauters, Rafael Valls and Frederik Veuchelen.
The event starts in Naples on Saturday and is exclusively live in the UK on British Eurosport.