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.
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."