While speaking on ABC Ballarat, Mr Merlino said the Department of Education was listening to concerns voiced by parents about merging four secondary schools into one.
He said of all projects in regional Victoria and the state "this is the most important".
Mr Merlino was asked if the Shepparton community was supporting the Super School on the back of the Nationals' decision to survey Greater Shepparton locals about their views.
"We've been engaging with the community for more than two years," Mr Merlino said.
"The National party want to play politics and this is their choice. They've represented that part of Victoria for many, many decades.
"It's difficult to talk about because our teachers and our principals do their very best but what we've had, not just for the last few years but for decades, is student outcomes in the Shepparton region that are so far below national minimum standards," Mr Merlino said.
When responding to why the plan was controversial Mr Merlino said the biggest questions raised had been based around transition.
"Change is difficult. A lot of questions from parents have been 'how does this impact my student'... how are you (Victorian government) going to support.
"That tells me parents care deeply about their children's education so I welcome those.
"We've been responding to the questions and concerns that have been raised.
"This is a project that needs to happen and we need to do this for kids in Shepparton, Mooroopna and that region."
Mr Merlino said at the Year 9 level, in three of the four secondary schools, 60 per cent of students were in the bottom quartile while the remaining school was at 46 per cent.
"This is despite the best efforts of our teachers and principals. You cannot tell me the kids in Shepparton are not as ambitious or capable as any other student in Victoria.
"I've got a responsibility as the Minister for Education, Suzanna Sheed is the independent Member for Shepparton, the parents, the educators all have a responsibility for those kids to do something about it," Mr Merlino said.
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