The school was locked down in November after police received a "credible threat" relating to the school.
"The threat made reference to Wellington High School, which was placed into partial lockdown for around one hour as a precaution while the incident was dealt with," police said in a statement at the time.
"We know this incident has been worrying and we urge anyone with concerns about their safety or the safety of others to speak to police immediately to report it."
Most details from today's hearing cannot be reported because heavy legislative restrictions surround Youth Court matters.
Chief Youth Court Judge John Walker allowed reporting of the fact the matter has now been referred to a family group conference, after which it will return to court.
Bail has been continued, with some variation to the conditions.
Wellington High School principal Dominic Killalea said on the day of the lockdown the situation was challenging and teachers and students responded "wonderfully".
"There were, of course, students trying to do exams and many of them may have been affected by the information being received this morning."
He said there was a derived grade process that could be used for students affected.