In the country's "family portrait" released by Statistics Canada, the government agency said it had counted 45,345 gay couples of which 7,465 had married after the inauguration of gay marriage laws in July 2005.
It was the first time the agency had counted gay married couples in the national census, carried out in 2006.
More than half, some 53 percent, of the gay married couples were men.
"Half of all same-sex couples in Canada lived in the three largest census metropolitan areas, Montreal, Toronto and Vancouver, in 2006," the study said, adding that "Toronto accounted for 21.2 percent of all same-sex couples."
Gay couples however only made up some 0.6 percent of all Canadian couples, a figure which compares with Australia (0.6 percent) and New Zealand (0.7 percent).
The census also revealed that more people are choosing to live together without exchanging vows, with the number of married-couple families only up 3.5 percent since 2001 to 6.1 million, compared to the numbers of common-law partners which had leapt 18.9 percent to 1.4 million.
The number of single-parent families also surged 7.8 percent to 1.4 million compared to the previous census carried out in 2001.
The figures were the third set of data to be released by Statistics Canada since last year's census of the country's 31.6 million people.