The issue concerns Springbok and Bath playmaker Butch James, who was due to feature at centre in today's clash with Wales before being withdrawn.
English clubs are not obliged to release players for a match that falls outside the recognised IRB June playing window. The SARU had hoped to secure James' release by virtue of clauses in his contract but their request was rejected by PRL, the umbrella organisation for the Guinness Premiership clubs.
The ruling has upset the SARU, whose president Oregan Hoskins was left further infuriated after Saracens hooker Schalk Brits was allowed by his club to play for the Barbarians.
"SARU, Bath and Butch were all keen to see Butch play but the rule has been strictly enforced," said Hoskins.
PRL responded by saying that they will take the matter up with the IRB. A statement read: "PRL regrettably has to make a formal complaint to the IRB alleging a breach of international regulations by SARU through their actions and statements this week.
"These actions and statements have been repeatedly directed against Bath and PRL and seem to have been designed to put unfair pressure on the player and his club, who have acted in accordance with the IRB's regulations."