"The team has just returned from South Africa, and we are discussing all available details with team management," the NZRU said in a statement.
"Our understanding of the matter is that the allegation was focused on one player."
Neil Sorensen, the NZRU general manager of professional rugby, said all members of the nation's Under-20 squad had returned home.
"The team and team management complied with local police requirements and co-operated fully and assisted them with their inquiries, after which police advised they were happy for all members of the team to travel home," Sorensen said.
"Neither team management, nor NZRU have been contacted by the local authorities since then or advised of any further issues or inquiries.
"If we are contacted, we will co-operate and help in any way we can."
Colonel Vish Naidoo said earlier police were called to the New Zealand team's hotel in Cape Town on Saturday morning when a 22-year-old woman claimed one of the "Baby Blacks" had raped her.
"Police forensic experts were on the scene at the hotel scouring the crime scene and taking samples on the spot."
Naidoo said the charge was being investigated.
The New Age reported that the New Zealand High Commission held top-level negotiations with police about the incident and to secure the whole team's safe passage from South Africa on Saturday night.
The New Zealand side lost 22-16 to the Baby Boks at a packed Newlands Stadium in the final of the IRB Junior World Championship on Friday evening.
Source: http://www.sport24.co.za