Victorian Department of Education data shows GSSC recorded a drop of more than 200 students from last year, including 160 fewer year 7 students.
Before the merger, Shepparton High School, Mooroopna Secondary College, McGuire College and Wanganui Park Secondary College had 2543.5 full-time students enrolled as of February 2019.
But the 2020 figures show the merged super school had 2334.2 full-time students enrolled as of February 2020, representing a 209.3 decrease.
Save our Schools chair Robyn Boschetti said she was concerned that if students continued leaving to other schools, nearby high schools would reach capacity, eventually forcing some students to attend GSSC.
“People haven’t got a choice — where do you put your kids?" she said.
“I know people who have been trying to get (their kids) into Notre Dame College or St Anne's College, and they’re trying so hard to get them into these schools so they don’t have to go to the super school.
“We don’t want one school for 3000 students, we want a few schools so we can have a choice where we send them.”
But the Department of Education said "fluctuations" in enrolments were no surprise.
“Fluctuating enrolments are to be expected during the initial years following a merger while a new school builds its reputation and identity,” a spokesman said.
“We anticipate strong enrolments at Greater Shepparton Secondary College from 2021."
The spokesman said Shepparton and Mooroopna secondary schools experienced a fall in enrolments every year from 2010 to 2019.
“Below-average public secondary student outcomes and declining enrolments at Shepparton and Mooroopna secondary schools are among the key factors behind the investment in the Shepparton Education Plan and the development of Greater Shepparton Secondary College,” he said.
GSSC is on track to be completed by the beginning of 2022, having recently received $119 million in Victorian Government funding.
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