Iran take its turn at the helm of the organization later in May, prompting Foreign Affairs Minister John Baird to announce Tuesday that Canada will sit out the sessions during their term.
Giving Iran the position, even if it is only temporary, makes a mockery of disarmament issues, said Baird spokesman Rick Roth.
"In Iraq, Syria, Lebanon and elsewhere, the regime is working directly against global disarmament goals and subverting the fundamental principles of this committee," Roth said in a statement.
"Iran's leaders blatantly ignore their international obligations, all while undermining regional security."
Iran presides over the 65-nation Conference on Disarmament from May 27 until June 23.
The rotating chairmanship is largely ceremonial but high-profile; the conference is considered the world's most important disarmament negotiating forum.
In its 50-year history, it has been responsible for negotiating the international non-proliferation treaty, as well as conventions on the prohibition of biological and chemical weapons.
But the conference has been locked in a stalemate for two decades, failing to reach new arms control accords.
Iran's election to the presidency of the conference is its right, according to existing rules and procedure, said Alireza Miryousefi, a spokesperson for the Iranian mission to the UN.
"During its presidency, the Islamic Republic of Iran would focus on promoting the goals and objectives of the Conference on Disarmament through according the highest priority to nuclear disarmament and the total elimination of nuclear arsenals of the nuclear-weapon states in an irreversible, transparent and internationally verifiable manner," Miryousefi said in an email.
Iran has fully compiled with its international obligations, including those negotiated by the conference, Miryousefi added.
It's not the first time Canada has boycotted the conference.
In 2011, North Korea took its turn as temporary president, prompting Canada to sit out then as well.
The U.S. didn't follow suit in that instance, saying they didn't consider the regime's involvement to be a "big deal." But they will back away during Iran's term, American officials said Monday.
They argued that countries under UN sanctions shouldn't be allowed to hold such positions.
The UN Security Council has imposed four rounds of sanctions against Iran because of concerns it is seeking to develop nuclear weapons and its refusal to suspend uranium enrichment.
Iran claims its nuclear program is peaceful and exists only to produce energy for civilian use.
It denies any secret work on nuclear weapons, saying the allegations are based on falsified intelligence from Israel and the West.
UN spokesman Martin Nesirky, asked about Secretary-General Ban Ki-moon's views on Iran's upcoming presidency, said member states decided on a monthly rotation and it's up to them to make any changes.
"The secretary-general simply wants to see movement on the conference on disarmament," Nesirky said.
"He has been quite critical ... on the lack of progress."
— with files from The Associated Press