Harper was asked during a news conference with Trinidad and Tobago's prime minister about concerns with the timing of the arrests. He was also asked about when it's appropriate to talk about the root causes of involvement with terrorism.
The Conservatives had taken Liberal Leader Justin Trudeau to task when he suggested last week it was important to look at the root causes of the Boston Marathon bombings after offering condolences and support to the victims. They said he was trying to rationalize the bombings or make excuses when the Liberal leader said the bombings happened because someone felt excluded from society.
"I think, though, this is not a time to commit sociology, if I can use an expression," Harper said. "These things are serious threats, global terrorist attacks, people who have agendas of violence that are deep and abiding threats to all the values our society stands for.
"I don't think we want to convey any view to the Canadian public other than our utter condemnation of this kind of violence, contemplation of this violence and our utter determination through our laws and our activities to do everything we can to prevent it and counter it," Harper said.
On CBC News Network's Power & Politics on Thursday, Conservative MP Pierre Poilievre was asked by host Evan Solomon to elaborate on Harper's comments and what is wrong with trying to understand why people turn to terror.
"Nothing, but that's not the issue," he responded. Poilievre said Trudeau mishandled his response to the Boston bombings.
"The root causes of terrorism is terrorists," he said. "That's how we respond."
The two accused men are Chiheb Esseghaier, 30, of Montreal, and Raed Jaser, 35, from Toronto. They have been charged with conspiracy to carry out a terrorist attack and "conspiring to murder persons unknown for the benefit of, at the direction of, or in association with a terrorist group." The two men arrested are not Canadian citizens but were in the country legally, according to police.
Canadian and U.S. law enforcement agencies have been co-operating on surveillance of the suspects on both sides of the border for some time.
The FBI had asked Canadian authorities multiple times over recent months to hold off on the arrests while it continued to probe who else might be involved. The RCMP had earlier met the requests but then moved ahead with the arrests on Monday.
"It is law enforcement agencies, including obviously the Royal Mounted Canadian Police, CSIS and others, but particularly the RCMP, that make decisions on operational police matters," Harper said about the timing of the arrests. "And obviously they have worked very closely with their American counterparts and I congratulate them for that work once again."
Harper also said that "radicalization" is something that is followed closely.
"Our security agencies work with each other and with others around the globe to track people who are threats to Canada and to watch threats that may evolve," he said.
Toronto Imam Yusuf Badat, of the Islamic Foundation of Toronto, told CBC's Evan Solomon that RCMP officers said they received tips from the Muslim community that led to the arrests.
RCMP spoke to community leaders before the news briefing held Monday about the arrests. Badat said none of the community leaders that were present at the briefing had heard of the two men arrested.
Some people who know the men said their behaviour had changed in recent months and one said that Jaser's father was concerned his son was becoming too "rigid" in his religious beliefs.
Trinidad, Canada pledge greater economic ties
Harper was asked about the terror-related arrests during a joint news conference with Kamla Persad-Bissessar, Trinidad and Tobago's prime minister. Harper told reporters that the two leaders reaffirmed their commitment to increase trade and investment ties between Canada and Trinidad.
Trinidad is Canada's second largest trading partner in the Caribbean and Harper said increasing the relationship is a priority for both countries.
"We have taken steps to increase cooperation between Canada and Trinidad and Tobago in the areas of trade, security and academia," Harper said.
A number of memorandums of agreement were signed including one that will see the Caribbean nation take part in military training.
Later Thursday night in Toronto, the two prime ministers will attend the Trinidad and Tobago Canadian Community Reception, and Harper will deliver remarks.
Persad-Bissessar came to Canada with members of her cabinet, including the ministers of justice, trade, energy and transport. Business leaders from Trinidad and Tobago are also visiting Canada as part of a trade mission in Toronto.