The Ministry of Justice had admitted there was a communication error and was working to ensure it did not happen again.
The youths were arrested early Wednesday morning and were kept in custody to be brought before the court that day.
However, the court heard that despite waiting in the court cells all day on Wednesday, their cases were not called.
They were taken back to the police station cells at the end of the day. The court heard they did not have to spend the night, but only thanks to the after-hours actions of Oranga Tamariki staff members who took them to a youth justice facility.
On Thursday morning, the youths were brought back to the court and appeared before Judge Maree Mackenzie.
When Judge Mackenzie saw the first youth and learned he had spent the entire day before waiting in cells, she said: "This is a complete violation of his human rights. I am quite frankly horrified."
Judge Mackenzie said she and another judge were available the day before and she demanded to know from the court what went wrong.
"My mouth is wide open like a guppy . . . I will follow that up with the court. Young people are not adults and have to be treated differently."
Oranga Tamariki representative Sonia Wilson said she became aware the youths had not been dealt with by the courts and were taken back to the Rotorua police station.
Wilson told Judge Mackenzie given the youths were not meant to be kept in police custody for longer than 24 hours, she and a staff member went to the police station at 7.15pm on Wednesday and got them released into their custody and personally drove them to the Te Maioha o Parekarangi, the youth justice residence on the outskirts of Rotorua.
Judge Mackenzie thanked Wilson for her actions, saying she should not have had to do that.
The judge also apologised to the youths' families, who were in court, and explained it would not have been a result of "bad faith".
"It is maybe they thought the judges were too busy or did not understand (youths were a priority)."
The Rotorua Daily Post asked the Ministry of Justice why the youths were forgotten.
Chief operating officer Carl Crafar said in a statement young people who had been arrested were prioritised by the courts.
"Unfortunately due to a communication breakdown in this case, the correct procedure for processing a youth arrest was not followed," the statement said.
"The ministry is in discussions with our justice sector partners about how this communication breakdown occurred and what is required when there are youth arrests to ensure this doesn't happen again."