Chiheb Esseghaier, 30, a graduate student in Montreal, dismissed his court-appointed lawyer, telling her he did not need her, The National Post reported.
"The conclusions are drawn from facts and words that are not what they appear to be," Esseghaier said in a Montreal courtroom.
Raed Jaser, 35, of Toronto appeared calm and confident as he stood in front of a magistrate in a packed courtroom in Old City Hall, the Toronto Sun reported. He spoke only to confirm his identity.
Jaser was ordered held in custody. The magistrate also barred him from communicating with his co-defendant.
Esseghaier was arrested Monday at a McDonald's restaurant in Montreal, flown to Toronto and then returned to Montreal.
Faouzi Bellili, another Tunisian student in Montreal, told The (Montreal) Gazette he has known for more than a year of Esseghaier's extreme political views.
"He was saying things like, 'When you pay taxes here, you're only helping Canadians,' and I didn't really understand and wanted to say, 'If you don't like it, leave the country'," Bellili said in a telephone interview, describing a conversation they had outside a mosque. "I realized he had a very different vision and that I was wasting my time talking to him."
The Royal Canadian Mounted Police began the investigation based on a tip from an imam in Toronto, The (Toronto) Globe and Mail reported. The two men allegedly planned to set off a bomb that would derail a train from Toronto to New York City while it was still in Ontario.