"In some of these markets we're seeing improvements," CMHC chief economist Bob Dugan told reporters Thursday.
However, Dugan said the agency will keep monitoring the two markets closely.
"We don't want to take our eye off the ball just yet, because we don't want to run the risk of missing something," he said.
The study says the majority of other housing estate markets across the country are relatively stable.
Toronto is identified as facing a moderate risk, as the number of condo units under construction is near historical highs and price growth is outpacing growth in personal disposable income.
A risk of a correction is moderate in Montreal as well, as demand from first-time buyers is waning while the number of condo units currently under construction is near an all-time high.
Meanwhile Vancouver, one of the country's hottest real estate markets, is rated as low risk. Despite the fact that house prices in Vancouver are growing rapidly, demand is supported by the city's growing population and increases in personal disposable income.
"It's always been one of those markets that's had a higher average price, but high average price in and of itself isn't an indicator of overvaluation," said Dugan.
CMHC's House Price Analysis and Assessment aims to identify potential risks in Canadian real estate by evaluating economic, financial and demographic factors.