"Sadly guys, I’ve had a minor setback on my road to recovery," Van Niekerk added on Twitter.
"I’ve been pushing myself a bit too hard in training so that I can make a memorable comeback but I have picked up a bone bruise on my knee so won’t be participating in the upcoming @Diamond_League events."
While the Doha world championships are not until late September and Van Niekerk has already qualified as the reigning world champion, the injury raises questions about whether he will try to make a comeback at all in 2019 and instead prepare to defend his Olympic title in 2020.
Van Niekerk, 26, did not compete in 2018 after tearing his anterior cruciate ligament (ACL) in a celebrity rugby match in 2017.
He has run only one 400 metres this year, clocking 47.28 seconds in February. His world record from the 2016 Rio Olympics is 43.03.
"I will review my competition schedule with my team and together with my coach (Ans Botha) we will decide where and when to race," Van Niekerk was quoted as saying in his agent's statement.
Van Niekerk remained "hopeful" of targeting a third world title, the statement said.
“He had MRI scans which showed the ligaments and meniscus in his (right) knee were fine but unfortunately he picked up a bone bruise which has set him back five or six weeks," the statement added.
(Reporting by Gene Cherry in Raleigh, North Carolina; Editing by Clare Fallon)
