The Dimension Data rider, who last competed at the Milano-Sanremo, has been hampered by pain felt in his right ankle.
The discomfort was first felt on the penultimate stage of Tirreno-Adriatico in March and has hindered the sprint ace since.
“The injury was thought to be resolving but has unfortunately flared up again during training,” said team doctor Jarrad Van Zuydam.
“Further investigation and treatment is necessary over the coming days to resolve the injury before Mark returns to racing.”
His focus is now on the Tour de France where he will be aiming to add to his 30 stage victories.
Cavendish had also been due to ride today’s Scheldeprijs, but was taken off the provisional start list this week.
Belgian Tom Boonen, who took second last year in the Paris-Roubaix, will try to bow out of his final cycle race with a record fifth victory.
The Quick-Step Floors rider has also achieved three Tour of Flanders wins, three Gent-Wevelgem wins, five E3 Harelbeke/Prijs Vlaanderen wins, two Kuurne-Brussel-Kuurne wins, six Tour de France stages, two Vuelta a Espana stages, two national titles and a world title.