The 26-year-old is suffering from a sinus infection.
"Now I have a course of antibiotics," he told De Telegraaf. "Wednesday I'll go explore the course, because I still want to know what the new finale will look like."
The 2012 Tour of Flanders will not be including the famous Muur van Geraardsbergen climb after race organisers announced that they have designed a new finale for the race, which will now finish in Oudenaarde instead of Meerbeke, where it has ended since 1973.
Boom is hoping to have recovered in time for Paris-Roubaix the following week, where he finished 12th in 2011.
"I do not know whether I'm all right, but next week in Paris-Roubaix, I expect that to be sure, " he explained.
The current Rabobank squad for the Tour of Flanders is: Lars Boom, Carlos Barredo, Matti Breschel, Tom Leezer, Bram Tankink, Maarten Tjallingii, Dennis Van Winden and Maarten Wynants.