The little girl required extensive surgery for her injuries but was discharged from hospital yesterday.
Police said a detailed examination of the crime scene was carried out over three days and a team of between 20 and 30 staff had been working on the investigation.
"As a result of this work police became interested in a 16-year-old youth from Turangi and negotiated his attendance at Turangi police station this afternoon. He has subsequently been charged with sexual violation, aggravated wounding and burglary,'' police said in a statement.
He will appear in the Youth Court at Taupo at 2pm tomorrow.
The family of the girl had been advised of the arrest.
"They are overwhelmed and relieved by news that someone has been charged, but their priority remains the health and wellbeing of their daughter. They wish to maintain their anonymity and privacy and intend to continue their holiday in New Zealand. They have also expressed their thanks for the overwhelming support of the police, Waikato Hospital staff and Victim Support.''
In a statement, the parents said: "We are very relieved at this news and want to thank the police, particularly those who gave up their precious time when they would usually be with their families. We can't thank them enough. They were meticulous, thorough and caring. They are a credit to New Zealand.
"We heard today too that the Turangi community raised more than $13,000 for our daughter. We are again amazed at the generosity of New Zealanders and thank this community. We know what happened was a random act of evil and will never hold Turangi responsible for it. We feel their love and support tonight.''
Detective Inspector Mark Loper said: "I am extremely pleased for the family of this little girl and for the good community of Turangi that we have been able to make an arrest within a week of the incident.
"This case has really touched the hearts of so many people in New Zealand and staff from the police and ESR have worked with dogged determination to bring about an early resolution.
Mr Loper also thanked the people of Turangi.
Waikato District Health Board said the girl's family had been inundated with letters and emails from people who were appalled and ashamed at the attack.
They wanted to assure the family the attacker was not representative of all New Zealanders.
One writer said: "Really Really sorry this happened to you I am disgusted at some of the people in our country I feel ashamed to be a New Zealander. Hope the wee girl makes a full recovery and that your family see that New Zealand is a beautiful place with friendly caring people not monsters."
Another writer said they were "humiliated, sad, and totally devastated" that the attack could happen in New Zealand.
"Our hearts go out to you at this time, and we sincerely hope you don't think that New Zealanders are all like this animal who attacked your daughter."
All New Zealanders were united in their anger and shock at the attack, a writer said.
"Kia-ora to the little girl who has experienced something so awful that we all in New Zealand are hanging our heads in sorrow...
"We are is awe of how you have coped with this tragedy and wish you much joy in your life ahead.
"Time will dull the memory and one day we hope you can return to enjoy more of what New Zealand has to offer."
