Gilberte Bussiere, originally from Asbestos, Que., was kidnapped along with two Italian priests before dawn Saturday in their residences in the small parish of Techere, in the country's north.
"It is with great concern and sadness that we have learned of the kidnapping," the congregation said in a statement.
After teaching in Quebec for two decades, Bussiere left for Cameroon in 1979 and has been there ever since working as an educator.
When she came back to Canada for health reasons last year, the congregation said Bussiere "expressed eagerness to return to the country and the people she loved."
Italy's foreign ministry identified the priests as Giampaolo Marta and Gianantonio Allegri, but declined to give other details to avoid compromising efforts for the missionaries' release.
It noted that its website cautions against travel in the area, 30 kilometres from the border with Nigeria "in consideration of the risk of kidnappings due to presence of jihadist elements coming from Nigeria."
A spokesperson for Foreign Affairs in Ottawa said they were aware of the report.
"We are pursuing all appropriate channels to seek further information and are in close contact with Cameroonian authorities," the spokesperson said in an email.
A Vatican spokesman, the Rev. Ciro Benedettini, said the priests were assigned from the Vicenza diocese in northern Italy.
The missionaries who were kidnapped "are greatly loved and greatly appreciated," Vicenza diocese spokesman the Rev. Alessio Graziani said. "The people there have great esteem for them."
Benedettini said Pope Francis was told early Saturday about the abduction, was praying for the three and "expressed hope for a solution."
Vatican Radio said the three were seized by the armed kidnappers in the diocese of Maroua.
"It isn't ruled out that those who carried out the abduction belong to the Islamic fundamentalist group Boko Haram," Vatican Radio said. Diocesan officials said no one had claimed responsibility for the abductions.
Vatican Radio broadcast an interview with an unidentified priest from Vicenza who said the kidnappers took the Canadian woman, but left nuns from Cameroon who work with the Italian priest.
- with files from The Associated Press