Both players have been included in the 15-man squad for the global tournament but only played in one fixture each in the recent five-match ODI series against Australia.
Nortje bowled five overs in the second match in Bloemfontein before leaving the field with back spasms and has been receiving treatment since.
Magala only bowled four overs in the third ODI in Potcheftroom but has been battling a knee injury that has ruled him out at the start of the home summer.
Speaking to the media after the Proteas sealed a 3-2 come-from-behind series victory over the Aussies at the Wanderers, Walter said the management would like clarity on the injuries before they depart for the World Cup in India on Friday.
"We are continually taking stock as to where both of those players are," Walter said. "The fact that they weren't playing today with a week to go before we board the plane for the World Cup is obviously a cause for concern.
"We would have wanted them out there. There are complications around taking players that are injured into a World Cup because then you have to provide a medical reason to be swapped out."
Should either Magala or Nortje be ruled out it is likely that all-rounder Andile Phehlukwayo will be a strong candidate to board the plane to India.
Phehlukwayo was not named in the initial World Cup party but showed his capabilities in the final ODI against Australia, striking 38 not out off just 19 balls to finish the innings strongly and then took 1-44 with the ball in a 122-run victory.
Walter said: "Andile is one of a couple of guys who are part of a broader squad and today he showed us, especially with the bat, what we have seen in terms of his capability.
"That knock, you can look at it, and say it was match influencing. A total of 270 looks different to a total of 315 and he was a massive role-player in that. He took an important wicket with the ball as well. I am very happy that Andile was able to deliver that performance today."
The Proteas have two warm-up fixtures in India before their World Cup campaign gets underway on 7 October against Sri Lanka in Delhi.