Players from outside the selected 31-man squad took part in a practice session on Wednesday ahead of the Pool A game against England on Saturday.
"World Rugby is satisfied no deliberate breach was intended, and in addition to the formal warning to the Welsh team, all participating teams have been informed that additional players from the extended national team squad, including potential injury replacements, may not participate in any training sessions," World Rugby said in a statement.
Wales coach Warren Gatland was mystified by the warning.
"We haven't broken any rules," he said. "Apparently we have broken the spirit of the rules. What that means we don't know. I don't know what we have done wrong."
Wales, who have suffered a number of injury problems, have contacted tournament organisers about the possibility of bringing in a front-row replacement after props Paul James and Samson Lee sustained injuries in their opening win over Uruguay.
"We’re waiting to make that call when we need to," assistant coach Rob Howley said.
"We have already contacted Rugby World Cup and there is special dispensation for front rows which allows us to bring someone in even 24 hours before a game."
Lee was named on Thursday among the Welsh replacements for the England game.
(Reporting by Ed Osmond,; Editing by Tony Jimenez)
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