SARU is now attempting to recover from the tumultuous tenure of former president Brian van Rooyen. His tenure as SARU (then SARFU) president began in 2004, after the debacle of the 2003 World Cup, which saw the Springboks exit in the quarterfinals, and the scandal of Kamp Staaldraad, the training camp run by then-Boks coach Rudolph Straeuli. Straeuli would resign, as did Rian Oberholzer, the managing director of South Africa Rugby (Pty) Ltd, the commercial arm of SARFU. Soon afterwards, SARFU president Silas Nkununu, facing a strong reelection challenge, withdrew from consideration for election, and van Rooyen was elected president. He soon became a highly polarising figure in South African sport, with detractors accusing him of financial shenanigans, favouritism, and general mismanagement. His management style was also widely perceived as autocratic.
One of the major gripes against the van Rooyen administration was the allocation of Springboks Test matches. The KwaZulu-Natal union did not receive a Tri Nations Test in either 2005 or 2006; the Free State union received no Tests in either year. Both unions, vocal opponents of van Rooyen, accused him of punishing them for their opposition.
However, the biggest bone of contention surrounded the expansion of the Super Rugby competition. SANZAR, a consortium of the South African, Australian, and New Zealand governing bodies, expanded their Super 12 competition to 14 teams, a change that took effect in 2006. South Africa was entitled to add one franchise to the four from the Super 12 era. In a controversial move, the Southern Spears franchise was assured a place in the 2007 and 2008 competitions, with an increasingly unpopular promotion/relegation system established to keep the total of South African Super 14 teams at its allotted five. Van Rooyen was widely viewed as being responsible for this arrangement, which was generally opposed by the existing Super 12/14 sides.
The South African government attempted to step in to address perceived problems within van Rooyen's administration, but he survived two years of attempts to oust him. Finally, at the 2006 SARU General Meeting, van Rooyen was voted out in favour of Oregan Hoskins, who immediately promised a more decentralised management style. Shortly after the election, it was alleged that van Rooyen had offered a bribe of ZAR 3 million (USD 485,000) plus a Springboks Test against France to the Free State union in exchange for the union changing its vote in the presidential election in his favour. Hoskins soon announced that a planned investigation into van Rooyen's administration would go forward. As for the Spears issue, the SARU Presidents' Council issued a recommendation on 24 March that SA Rugby revisit the decision to admit the Spears. On 19 April, the decision to admit the Spears was officially overturned.