The Het Nieuwsblad newspaper says the 74-year-old Merckx crashed on Sunday and was admitted to a hospital in Dendermonde.
Merckx is regarded by many as the greatest cyclist ever. He won five Tour de France titles and a record 34 stages.
The 2019 Tour de France began in Brussels in July and feted Merckx to mark the 50th anniversary of his first Tour victory.
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Known as "The Cannibal" for his appetite for winning, Merckx also won five Giro d'Italia titles, one Spanish Vuelta and a string of one-day classic races.
Het Nieuwsblad reports Belgian cycling great Roger De Vlaeminck was also admitted to hospital on Saturday with a fever and will stay there for a further 48 hours, believed to be from a virus in the blood.
"Considering all circumstances, I am doing well right now," the 74-year-old Vlaeminck told the newspaper. "The fever has subsided and I also feel no pain. Although it has settled a bit on my neck muscles."
