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De Villiers was commenting after the end of the Springboks' northern hemisphere tour that concluded with 10-15 loss to Ireland in Dublin on Saturday.
Some of the squad members returned from Europe on Monday but a host of players have remained in London for the Barbarians match against the All Blacks next weekend.
"It is imperative that we monitor the players training and playing load with their longer term well-being in mind," said De Villiers.
"This (2009) has been a very long season and it is evident that many players are mentally and physically fatigued.
"The biggest concern, however, is the cumulative effect of the amount of rugby that Springbok players have played over the past three years, as we know that this puts them at risk to injury in the following year.
"In order to get best out of our players for 2011 we will have to manage their training and playing times during 2010.”
De Villiers said that SA Rugby would soon hold a workshop with the medical and conditioning staff at the provincial unions to discuss how the country can get the best out of the players whilst also ensuring their longer term well being.
"A number of players have played over 2 000 minutes of rugby this year encompassing the Super 14, Lions Series, Tri-Nations and Currie Cup.
"We need a unified approach to address this and a host of other matters relevant to the welfare of our top players.”
On the 2009 tour, De Villiers said that while results had not gone South Africa's way it had provided a valuable insight into the challenges faced in the next two years as well as into the quality of young players coming through the ranks.
"It is never nice to lose but we have learnt a lot from this tour. Regardless of the disappointing end to the year you cannot take away the successes that made this team the best in the world in 2009.
"We have been able to identify our key focus areas for next year and we have been able to identify some of the players who will take the Springboks forward after 2011," De Villiers said.
Springbok captain John Smit added: "Although we did not achieve all of our goals on this tour, this team can hold their heads high for what has been achieved over the past year.
"It is a privilege to be part of such a special group of players and I have no doubt that they will put the disappointment behind them and be back stronger and more determined in 2010," Smit said.
