Earl Spencer also revealed that Prince Charles has spoken to him just once since Diana was killed in a Paris car crash five years ago.
And Charles had never visited Diana's grave on an island at the Spencer family estate, the earl said in an interview with the Guardian newspaper.
At Princess Diana's funeral, Earl Spencer pledged that the princes' "blood family" would continue the "imaginative, loving way" in which his sister was "steering" them through life.
"What I can say is that they may not be encouraged to stay in touch with their mother's side of the family," he told the Guardian.
Protection
The earl said he had met Prince Charles at a reception in South Africa, the only time the pair had met since Diana's funeral.
Earl Spencer, who was named by Diana in her will as her children's guardian, declined to say how often he saw the boys although he added: "I haven't seen William for a while."
"I have seen Harry very regularly. There are also text messages, e-mails - there are all sorts of communication rather than just physical contact and there's nothing I wouldn't do for them.
"I've seen the prime minister about their privacy. I've dealt with newspaper stories that were going to come out that I thought were particularly unfair on them behind the scenes.
"They are two young men who have very full social diaries and an active life with their father's family and I understand all that. I was not saying I was going to nanny them, I was just there to protect them and give them a different direction if they needed it."
'A private matter'
Another aspect of Diana's legacy was that William would be allowed to marry who he chooses, which Earl Spencer believes will be allowed to happen.
He said: "I think he's got it in him to choose who he wants to marry. I don't think he'll be told."
Earl Spencer - who said the interview would be the last he would give on the subject of his moving speech at Diana's funeral - also said he was tricked into letting the princes walk behind their mother's coffin along the funeral route.
Prince William and Prince Harry were just 15 and 12 at the time.
"I was told that they wanted to do it and that they would like it if I were there. I now know that's not true," he said.
"I thought that was where tradition and duty went too far against human nature."
St James's Palace press office would not be drawn on Earl Spencer's comments, saying: "This is a private family matter."