Education Minister Chris Hipkins said while universities were autonomous, he would not have made the same decision as Thomas.
"I think the universities should be free to make these decisions. I think in this case they've made the wrong decision but that's a matter for the university," Hipkins said.
Hipkins said while he "completely disagreed" with Brash, he should be free to speak.
ACT leader David Seymour called for Thomas's resignation.
"After veiled threats from a left-wing thug in a letter to the vice chancellor, she capitulated this morning and prevented Dr Brash from speaking on 'security' grounds, Seymour said.
Hipkins said he couldn't conceive of any security grounds that might need the event to be cancelled.
"I find it pretty difficult to believe that their security concerns would be of the kind of threshold you'd need really to justify the type of action Massey's taken."
In a statement announcing the cancellation, Massey University referenced Brash, a former politician and Reserve Bank governor, as a supporter of Southern and Molyneux.
Brash is a member of the Free Speech Coalition which was founded recently by a group of New Zealanders following a decision by Auckland Council to ban Southern and Molyneux from its venues. The coalition argued the move breached the principles of free speech.
Brash said Thomas had no grounds to call him a supporter of Southern and Molyneux.
"Am I defending them? No. I am defending their right to speak."
Brash said what Thomas had done was "very, very serious".
"I understand David Seymour's call."
National leader Simon Bridges called it an "absolute disgrace".
"I think New Zealanders are a fair-minded people. We want people to be able to have their say and then make up our minds ourselves.
"This is a university and, hello, universities are places where we should be encouraging free speech, we should be allowing debate even on the most controversial of subjects."
Massey said club members approached university management concerned about their ability to keep the event secure after becoming aware of social media posts suggesting the event could lead to violence.
"The university considered providing additional security for the event, but decided the risk of harm to students, staff and members of the public was too great, particularly at time of heightened tension over the issues around free speech and hate speech.
Thomas said she supported free speech on campus but totally opposed hate speech.
"In my opinion the views expressed by members of Hobson's Pledge come dangerously close to hate speech. They are certainly not conducive with the university' strategy of recognising the values of a Tiriti o Waitangi-led organisation."
"It is clear there is heightened sensitivity and passion at this time, following the protests both against and in support of Ms Southern and Mr Molyneux's right to be heard. Our ultimate responsibility is for the safety and wellbeing of students, staff and members of the public on our campuses and under those circumstances cancelling the booking is the right thing to do. The members of the Politics Club have acted responsibly in raising their concerns with the university and are free to meet Dr Brash at another venue if they wish."
