A New Brunswick man has filed a complaint with Canada's air transport security authority after he says he was forced to remove his medical cannabis from its prescription container before boarding a flight.

Burton resident Laurie Manzer, who is a veteran and a campaigner for cannabis as a medication, uses the drug to deal with pain and anxiety from the injury that ended his military career.

On Monday, he was flying to Fredericton from Toronto through the Pearson International Airport, carrying about 30 grams of dried marijuana and 50 millilitres of cannabis oil.

"I have a lockable, smell-proof container that I put my licensed producer containers in to ensure absolute security," he said.

He said the container was labelled with his prescription.

"From what I understand, that's what they need to contain," he said.

When he got to security, the agent appeared "quite confused" by the container, Manzer said, and asked him to pour the marijuana into a plastic bag.

A photo of Manzer's medical marijuana and containers. (Facebook/Laurie Manzer)

"And I said well, the plastic bag says liquids, why am I putting dried medicine in there?

And he said, 'Well, that's the law,'" Manzer recalled.

After some discussion with agent, Manzer said he agreed to put his marijuana in the bag so he could get to his flight.

He decided to file a complaint with the Canadian Air Transport Security Authority (CATSA) over the incident.

Manzer said he's angry that he was put in a situation where he felt like he was being chastised even though he was obeying the law.

"Everybody's looking at me. I have certain conditions, like anxiety, that it really affects. And I don't like people being put in that situation," he said.

He said he decided to speak out about his experience because he's heard other stories of friends being "reduced to tears" at airports across the country when trying to travel with medical marijuana.

"It feels like we're all being villainized for this miraculous drug," he said.

Suzanne Perseo, a spokesperson for CATSA, said the agency is aware of Manzer's complaint and it is currently being investigated.

She said she could not comment further, other than to say all complaints are taken seriously.

According to CATSA's website, medical marijuana is allowed in carry-on baggage and in checked baggage, but travellers should be prepared to show medical documentation.