The programs, one in Moscow and the other in Ukraine, were set up in the early 1990s as a means to give weapons experts a place to work following the collapse of the Soviet Union.
But the work of both centres was given greater heft by G8 nations at the 2002 summit in Alberta, when the international body agreed to spend $20 billion on a ten-year program to combat the spread of weapons of mass destruction.
One of the four key pillars of the so-called global partnership was scientist engagement, via the redirection of former weapons scientists.
Since then, Canada has contributed some $60 million to International Science and Technology Center Moscow and the Science and Technology Center in Ukraine.
The need for the centres has passed, Foreign Affairs Minister John Baird said Tuesday.
"This is an organization which was established as the Cold War was ending to finance support in the former Soviet Union so that senior nuclear experts didn’t go and work in other parts of the world," Baird said.
"Given we're some 25 years out from that, the program has largely been successful. Most of the people have retired."
But a former Canadian ambassador for disarmament questioned why, if that's the case, Canada appears to be unilaterally abandoning a program that G8 nations championed as recently as the 2011 summit in France.
At that meeting, the G8 agreed to continue funding the global partnership for another 10 years and maintained that the scientist engagement strategy should remain a priority.
"It is a little curious, if that was all restated so recently, that there's been a decision that this work is now complete and not requiring any further support," Paul Meyer said.
"You would have thought if there was to be a determination of that nature, that it would be done more collectively by the G8 and other states that have co-operated with the global partnership endeavour."
Canada is still funding the global partnership; last year, the government announced $367 million over five years aimed at "building on past initiatives to enhance global weapons of mass destruction security."
"In effect we're actually spending substantially more than we did when that program was created," Baird said.
"We're just focusing it on where the new weapons of mass destruction are."
In the case of the Moscow centre, its future was placed in doubt two years ago when Russia announced its intention to withdraw.
Many took that as a sign of that program's eventual collapse, likely by 2015, which is the deadline Russia has placed for the conclusion of research programs taking place in its own country.
Canada's withdrawal is a logical step, suggested Elena Sokova, the executive director of the Vienna Center for Disarmament and Non-Proliferation.
"It's winding down," she said of the Moscow centre.
"And I think the purpose of the centre has been indeed served. I'm not suggesting there aren't problems to deal with but the instrument of the centre, the way it was established, the way it served needs, the idea is over. It's time to move on."
Meyer said that while the Moscow centre's demise have been hastened by Russia's withdrawal, there are still programs being undertaken by other countries and offers from them to play host to the facility headquarters.
Meanwhile, there have been no similar signals sent by the Ukrainian government about a desire to shutter the facility there.
It has, however, been struggling with funding shortfalls, in part because two years ago Canada dramatically scaled back funding to its operations, catching it off guard.
That announcement came just after Canada volunteered to help the organization restructure, according to documents posted on the Ukraine centre's website.
The decision to stop funding the two centres is the latest exit Canada has made from a multilateral organization or treaty that the Conservative government has declared past its best-before-date.
They include a decision to withdraw from a United Nations convention that fights droughts in Africa and elsewhere.
The government said membership was costly and of little benefit to Canadians.
Note to readers: This is a corrected story. An earlier version referred to chemical weapons