"I want to thank my family, friends and rugby community for supporting me during this time.
"I am disappointed that my special experience with the New Zealand Under 20 was marred by this allegation. My focus is now on getting on with playing rugby and I'll be working hard to prove that I can be a good asset for any team I am lucky enough to be involved in," he said.
NZRU General Manager Neil Sorensen said the NZRU was pleased that the South African authorities had now closed this matter.
"Nathan has already publicly acknowledged that he breached team rules when he allowed a woman to come back to his room after the Final of the Junior World Cup in South Africa in June.
"We consider Nathan's actions in breaching the team rules to be misconduct, and after considering all the circumstances we have decided that the matter will be recorded as a warning on his file.
"We now consider the chapter closed."
A family member at Harris's family home, who did not want to be identified, said the news was "a sigh of relief''.
"I'm not really going to say too much about at the moment. We might say something later on but at this time we're busy, he's in the middle of ITM Cup and stuff.''
He said Harris was trying to get on with his life. "From the start he's just tried to get on with it.''