The second group of about 15 people who held banners reading Free Speech, Not Drugs and chanted "We don't care, get off our campus, clear the air" said they were students opposed to people smoking marijuana on the university campus.
Police and the university's security team, Campus Watch, stayed away from the 2pm protest, during which people marched from the Union Lawn on campus to the university's registry building.
Protest organiser Cory Anderson said the recent arrests of three supporters of the pro-cannabis legislation reform group the National Organisation for the Reform of Marijuana Laws (Norml) at a Norml stand during a students association market day were a blatant attack on civil rights, especially the rights to free speech, freedom of expression and association.
The three men were arrested after being watched by plain clothes police officers.
The arrests were also an attempt by the police to "intimidate and quash" a political movement by arresting its leaders and those in association with them, he said.
Protesters held signs that read Defend Civil Liberties and chanted "Cops off Campus" as they marched.
Norml members have received increased publicity lately following the arrests, the subsequent trespass notices issued to the men and a police crack-down on a weekly "protest smoke-up" on the university campus.
Commerce student Lawrence Tuck, who marched with the anti-drug smoking group, said those marching with him were mostly members of a Facebook group he started recently in favour of a drug-free campus.
"We are a bunch of students who believe that drugs are illegal and should not be allowed to be used on campus.
"Anyone else using them would be arrested, but somehow these people have been afforded the right to break the law. It seems they have had the full support of the university too."
Supporter Rachel Schryvers said marijuana was an addictive drug and New Zealanders were constantly being reminded of the destructive side of addiction.
"So no to this is saying no to this particular culture."
There was a difference between freedom of speech and illegal activities on campus, Mr Tuck said.
Those on the other side of the protest said they wanted to make a point.
Student Paul McMullan said he joined the protest against the arrest of the activists to make a point about the "silly activity of the authorities" which he described as a "waste of time".
Law lecturer Andrew Geddes said it was pleasing to see students taking an interest in political matters.
"While I'm not fully sympathetic with the marijuana issue, people are actually going out and are willing to debate the issues.
It's a loss to the campus that these sorts of protests aren't held any more."
Mr Anderson said he was pleased with the way the protest went.
He believed more people would have turned out had the weather been better.
