Lee, 47, was unseated from his mount Ben Macdui before a race in Newcastle on Friday evening.
"He was taken by ambulance to the Royal Victoria Infirmary in Newcastle, where he is in intensive care with a neck injury," read a statement from the Injured Jockeys Fund on Saturday.
"He will undergo further tests today to assess the extent of the injury."
The Irishman won the Grand National in 2004 upon Amberleigh House.
Lee rode more than 1,000 winners over the jumps before switching to riding on the flat in 2012.
He also claimed the Ascot Gold Cup in 2015 on Trip To Paris.
