She confirmed a social media post made reference to taking a gun to the event which was scheduled for Wednesday.
There were also indications on social media of a demonstration, she said.
"We arranged a meeting with local police to discuss security. However, before that meeting could take place, and having considered all aspects of this, I made the decision to cancel the booking of the event on our campus.
"This is not the kind of decision that any VC takes lightly," Thomas said.
"Under the Health and Safety at Work Act 2015, Massey University has an obligation to ensure, as far as reasonably practicable, the health and safety of our workers, and anyone else who may be affected by our operations."
She said she stood by the decision based on the information available to her at the time despite the knowledge man staff members believed it was the wrong call.
Thomas said the experience highlighted the need to reassess how security threats were assessed and proposed the university engage in a series of discussions regarding freedom of speech and what it looks like on campuses.
She also rejected the notion the cancellation was related to anything other than security, saying she valued free speech immensely.