The prime minister last week criticized Liberal Leader Justin Trudeau for suggesting it was important to look at the root causes of homegrown terrorism.
Trudeau made the comments shortly after the deadly Boston Marathon bombings.
But today, at an Ottawa news conference with the visiting prime minister of Trinidad and Tobago, Harper was asked about whether it's appropriate to talk about the root causes of terrorism in light of the alleged Via Rail plot.
Harper responded that the alleged plot and the Boston attack are serious threats from people who have agendas of violence.
And he said he didn't want to convey any message to Canadians other than that the government utterly condemns such violence.
Two accused men, Chiheb Esseghaier of Montreal and Raed Jaser from Toronto, face several charges, including conspiracy to carry out a terrorist attack.
Harper congratulated Canadian and U.S. law enforcement agencies, which co-operated on surveillance of the suspects on both sides of the border.
But he said the timing of the arrests is an operational matter decided by police.