The ministry released little information about the case today, saying only that it was a 26-year-old member of the air force who has now been suspended from service.
The ministry says in a written statement that the suspect had been blocked from "all access to information, systems and locations."
The case would mark the first time a serving member of the Dutch armed forces has gone to Syria to join IS.
In a statement, Dutch Defense Minister Jeanine Hennis Plasschaert says it is "unpleasant if it turns out that somebody has joined up with evil while colleagues risk their lives for other people's freedom.