A $36.3 million Toowong high school expansion has been moved a few metres to save a 300-year-old tree of Aboriginal significance that would have been destroyed.

The news of the revision for Queensland Academy for Science, Mathematics and Technology follows the beginning of construction for the three-storey centre on Wednesday.

Education Minister Grace Grace described the outcome as "a win" but Save Toowong Creek spokeswoman Julie Lloyd said the minister needed to look at the bigger picture.

Ms Lloyd said the moving of the site by a few metres still affects the Toowong Creek and the natural habitat surrounding the tree and the expansion site.