Marx, one of two specialist hookers in the squad along with Bongi Mbonambi, was never going to be involved in Sunday’s second Pool B game against minnows Romania but the Springboks are worried about his availability for the remainder of the tournament in France.
Team officials did not elaborate on Marx’s issue but said an update on his fitness would be provided in the coming days.
South Africa do not have a third specialist hooker in the squad, with regular loose forwards Deon Fourie and Marco van Staden nominated cover.
The Stormers' Joseph Dweba was placed on standby when the squad was announced last month.
Fourie will be on the bench against Romania with Mbonambi starting the game.
Marx is the second key player under an injury cloud for South Africa after lock Eben Etzebeth left last weekend’s 18-3 victory over Scotland due to a shoulder issue.
Springboks director of rugby Rassie Erasmus said Etzebeth was likely to be out for seven to 10 days but should return for the crunch group game against world number one Ireland at Stade de France on September 23.