But a separate human-rights report also released Tuesday offers support to the Harper government's decision not to follow the United States, Britain and others in recognizing the disparate coalition of rebel groups.
The report from Human Rights Watch, the New York-based watchdog, says rebel fighters executed civilians in their custody and killed others with indiscriminate sniper fire and mortar attacks during a one-week battle in a mainly Christian village last month in northern Syria.
The report was unable to say which of several opposition groups was responsible for the abuses documented.
The memo, a briefing note on the Syrian crisis for Foreign Affairs Minister John Baird, reiterates Canada's opposition to recognizing the Syrian Opposition Coalition (SOC) in part because of concerns about extremist links. But it says the decision cost Canada membership in an 11-country group that is trying to find a diplomatic solution to the long-running civil war.
"This position is at odds with many of our closest allies," says the July memo, obtained under the Access to Information Act. The names of those allies are redacted from the document.
This "has meant that we are no longer a member of the Core Group of the Friends of the Syrian People, all of whom provide support directly to the SOC. However, the SOC has recently expanded its membership in response to concerns about its inclusiveness and diversity."
The Core Group is composed of the U.S., U.K., France, Germany, Turkey, Italy, United Arab Emirates, Saudi Arabia, Egypt, Jordan and Qatar.
The group met last month in London in a meeting chaired by British Foreign Secretary William Hague.
Hague said that the group committed to "put our united and collective weight behind a UN-led Geneva II process." Geneva II is the name for a peace process that could move forward if planned talks in that city next month actually materialize.
Canada is concerned the Syrian opposition contains militant Islamists and does not respect religious minorities.
In its Oct. 22 statement, the Core Group affirmed its backing of "moderate armed groups," and affirmed the need for a political solution.
On that same day, a Syrian rebel offensive on the mainly Christian village of Sadad, about 100 kilometres north of Damascus, was in its second day.
In its Tuesday report, Human Rights Watch identified the names of 46 civilians who it said were killed by rebel groups during a siege that lasted until Oct. 28.
The dead included a family of six, aged 16 to 90, whose putrid remains were found in a village well after government forces drove the rebels out of the village. One witness said the six dead were blindfolded, had their hands bound and were shot in the head.
Other civilians were killed because of indiscriminate shelling between government and rebel forces fighting in the village, while some were used as human shields, the report said. It also accused the rebels of looting and vandalizing three churches.
"Over the last two and a half years, Human Rights Watch has extensively documented abuses by government and pro-government forces during ground operations including executions, indiscriminate shelling and sniper attacks and the use of human shields," the report said.
"Human Rights Watch has also documented indiscriminate shelling and executions and kidnapping by opposition forces during ground operations."
Baird's spokesman Rick Roth described Tuesday's report as one more example of why Canada deplores "the senseless violence on both sides of this conflict, and the true tragedy of the innocent victims caught in the middle."
He reiterated Canada's concern over "the presence of radical jihadist elements" in the Syrian opposition.
"The decision not to recognize the opposition doesn't mean the minister hasn't engaged with them," Roth added. "He's met with the head of the Syrian Opposition Council on a number of occasions."
Syria's two-and-a-half year civil war has led to an estimated 100,000 deaths.