The 28-year-old Omega Pharma-QuickStep rider has missed the Gent-Wevelgem, Driedaagse De Panne and Tour of Flanders because of illness and his manager said the Manxman had been "weakened" by the virus.
"This flu has really weakened him," said team manager Patrick Lefevere.
"For a rider like him it makes no sense to start at only 50 per cent of his form so we decided to let him rest."
Lefevere added that he expected Cavendish to return in 2-3 weeks.
"We're also going to rethink our programme. He'll probably be at the Tour of Turkey, the Giro and the Tour of California."
Cavendish has won the Grand Prix de l'Escaut three times in the past.
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