"If I were a lawyer, I wouldn't go down the track of conspiracy theories if I wanted to have credibility," said Immigration Minister Jason Kenney, who said he was first briefed on the arrests Monday afternoon.
"Timelines for operational matters are dictated by our security and law enforcement agencies only, and we trust the good work that they do," said Julie Carmichael, a spokeswoman for Public Safety Minister Vic Toews.
Raed Jaser and Chiheb Esseghaier face charges including conspiracy to murder for the benefit of a terrorist group and participating in a terrorist group.
The charges outline that the alleged offences were committed between April 1 and Sept. 25, 2012, with an additional charge ending on Feb. 14.
Jaser's lawyer John Norris called the timing of the arrests "notable."
The Conservatives suddenly announced final debate on an anti-terror bill on Friday, which would revive measures that expired in 2007 including preventative arrests and special investigative hearings.
Government House Leader Peter Van Loan made no mention of the debate a day earlier, when he served notice of bills to be pursued in the coming week.
The last vote on the bill occured in February. It is expected to head to a third-reading vote on Wednesday. The debate pushed off the schedule a Liberal motion tackling the freedom of MPs to speak in the Commons.
"They've been very clear that there was no risk to public safety and it's surprising to say the least that this arrest would be made now, close on the heels of the events in Boston and timed perfectly with what was happening in the House of Commons yesterday," Norris said outside court Tuesday.
RCMP Sgt. Julie Gagnon said questions on the timing of the arrests and the debate on the Conservative anti-terror bill were for the government to answer.
Fraser Malcolm, a spokesman for Van Loan, said the House Leader had decided on the timing of the bill with no knowledge of Monday's arrests.
Also on Tuesday, the Conservative Party of Canada sent its supporters a new fundraising letter, the first line highlighting that the RCMP had "foiled a potential terrorist attack here in Canada."
It was the second fundraising letter in two weeks to centre around new Liberal Leader Justin Trudeau. Signed by the party's director of operations Jenni Byrne, the latest letter slammed a comment posted to a Liberal senator's Twitter account on Monday.
"Harper wants to align Canada with the US, wants the same republican policies: he will get also the same terrorists," reads the tweet from Senator Celine Hervieux-Payette's account.
Hervieux-Payette's office assistant later took responsibility for the tweet, and said he had mistakenly posted it to his boss' Twitter site instead of his own.
"Trudeau's Liberals think Conservative policies are the real 'root cause' of terrorism," Byrne wrote in the fundraising letter.
She added, "We need to make sure every Canadian knows that Justin Trudeau lacks the judgement and experience to be Prime Minister. Can you chip in $5 or whatever you can afford so we can keep the pressure on Justin Trudeau?"
Prime Minister Stephen Harper and the Tories have criticized Trudeau for musing on the "root causes" of terrorism, and individuals who feel excluded from society, just hours after the bombings at the Boston Marathon.
Liberal House Leader Dominic LeBlanc accused the Tories of playing politics with a tragedy.
"What’s interesting for us is that Mr. Harper probably holds the speed record in trying to exploit a tragedy like the Boston bombings for political advantage and this week he gets another prize for the record in terms of speed of trying to exploit for financial gain for his Conservative Party these tragic events," LeBlanc told reporters.
"There’s no depth to which he won’t sink to try and collect money for the Conservative Party, sending a fund-raising letter with a series of falsehoods, that’s only one of them, there are others, but we’re not particularly surprised or worried about that."
--With files from Joel Eastwood
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