Proudly South African was established in 2001, born out of the 1998 Presidential Job Summit convened.
"Now, nearly 20 years later, I lament the tortoise pace at which transformation at the highest level is being effected," he said in a letter to The Star's sister paper, The Cape Times.
Tutu criticised the SA Rugby Union (Saru) for the pace of transformation in the team, and said it was "particularly hurtful" to see the selection of black players as "peripheral squad members never given the chance to settle down and earn their spurs."
He said the country deserved a team that represented the "full spectrum of the rainbow that defines us".
"Surely, by the 20th anniversary of our freedom from enforced separateness, there are a couple of dark horses out there to run with the browns and the chestnuts in feature races?"
On Saturday, the Springboks take on Argentina in Salta in the Rugby Championship. Their starting 15 will include three coloured players, and the remaining 12 are white. Two of the eight players on the bench are black.