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The charges against Chiheb Esseghaier, 30, and Raed Jaser, 35, include conspiracy to carry out an attack and murder people in association with a terrorist group.
The two men charged with plotting to derail a Canadian passenger train will face a bail hearing Tuesday.
Investigators allege Chiheb Esseghaier, 30, and Raed Jaser, 35, were acting under "direction and guidance" from al-Qaeda operatives in Iran, AP reported.
But Iran hit back at the claims Tuesday, saying there was “no shred of evidence” to substantiate allegations of links to the terrorist group, reports by Iranian state media said, the New York Times reported.
“The Islamic Republic of Iran is the biggest victim of terrorism, but the extremist administration of Canada has put Iranophobia on its agenda over the recent years,” Ramin Mehmanparast, the Iranian Foreign Ministry spokesman, told a news conference Tuesday.
More from GlobalPost: Canadian police arrest two suspects in alleged bomb plot
Royal Canadian Mounted Police chief superintendent Jennifer Strachan said the attack by the two men, whose nationality was not disclosed, was in the "planning stage" and involved watching trains, routes and railways.
Reuters reported unnamed US officials claiming the attack would have targeted a rail line between New York and Toronto.
Speaking at a news conference, Mehmanparast said Iran opposed “any kind of violent action that endangers lives," the Mehr news agency reported.
"No shred of evidence regarding those who've been arrested and stand accused has been provided," Mehmanparast said.
Police stressed the arrests were not linked to the Boston Marathon bombings, which killed three people and injured at least 200.