Boys at a Melbourne high school claim they were told to put on shorts after showing up for their final day of classes wearing the traditional girls' uniform.

But the principal says the issue was not the boys wearing dresses, but that they were too short.

Bentleigh Secondary College year 12 students decided to swap uniforms for the day, in a final statement endorsing the Safe Schools policy of gender diversity.

But what was planned as an empowering message to younger students quickly turned sour.