"I was pretty happy with my performances yesterday, but they took a large toll on my body.
"After medical advice this morning I have decided to pull out and prioritise getting better as the next three weeks are incredibly important in selection for this year's world champs."
Drysdale said it wasn't a decision he made lightly.
"It's only the second time in 18 years I've had to withdraw from an event.
"I wish all my fellow competitors the best of fortune in the semis and finals [and] apologise for not fronting up, but look forward to some good racing over the coming weeks."
The double Olympic and five-time world champion was set to race in the same semi-final as compatriot Robbie Manson.
The pair are vying for the one world championship spot in Bulgaria during September.
The faster of the two at the World Cup in Lucerne, Switzerland on July 15 will earn that right.
Manson has had the edge this season as national champion. He was also the more dominant rower in the regatta's preliminary rounds.
He will contest the final at 10.33 tonight.
Drysdale's return comes on the back of a 10-and-a-half month lay-off following the Rio Olympics.
The process has seen him already lose at least 15kg from a peak weight of 120kg.
