"I definitely think those [old] flags should be banned," he told the RugbyFanz.com website. "It would be a step forward."
According to Ndungane, some South African fans still live in the past.
"The national anthem is no longer just Die Stem, it is a combination of N'kosi Sikilele Afrika and Die Stem," he says. "We need to look at the future."
Ndungane also said he believed that Springboks playing in Europe should be allowed to represent their country in Test matches.
"Look what they did at the World Cup," he added in reference to Springbok captain John Smit and others who are playing in Europe.