However, the cancellation of the event had created an opportunity to experiment with different performing arts, he believed.
It could boost the primary school version of the Stage Challenge and J Rock, Fresh Moves.
"It is now an opportunity to engage in school productions more. Maybe not the typical musicals, but more integrated productions like Stage Challenge."
Flanagan said the event directors had done an incredible job.
"I think they have set us up really well for dance and drama within performing arts nationally.
"Now that it has finished there is the opportunity to not reinvent Stage Challenge, but to come up with ideas for what dance and drama need now in 2018."
Starting the new school year without a Stage Challenge would upset a few students, Flanagan said.
"A lot of kids come to this school because of Stage Challenge. But our performing arts calendar is still really busy. Sheila Winn Shakespeare has become monumental for us."
Otumoetai College principal Russell Gordon hoped the cancellation of the popular event would only be temporary.
"It is a huge loss for schools and for students who can truly be themselves on stage or behind the scenes. It is a tragedy," he said.
Gordon said the Stage Challenge was an opportunity for students to learn life skills.
The Stage Challenge Foundation told the NZ Herald that income from this year's planned shows would not have covered costs.
The charity relied on government and corporate sponsorships, grants, participation fees and ticket sales to cover the cost of producing the events.
Foundation chairman Lester Taylor said a number of factors came into the decision.
Major production costs such as venue hire, staging, lighting and sound had increased, he said.
"The current economic conditions would make it extremely difficult for the corporate sector to sponsor the event."
Stage Challenge - and later J Rock - have been highlights of school performance calendars since 1992.
The Stage Challenge incorporated performing arts such as dance, music, design and drama within an eight-minute performance while J Rock gave primary and intermediate pupils the chance to express their creativity through the same artistic channels.
Each year about 200 schools, 16,000 participants and an audience of 25,000 people would turn out for the events, held at more than 10 venues nationwide.
Additional reporting NZME
