In a sober interview on CBC Radio's The House, MacKay said a mission as complex as Afghanistan "always causes pause for reflection."
MacKay said he wished, in some ways, that Canada had "provided more equipment, helicopters, mine-clearing equipment in the early days."
"I don't think the ferocity of the mission perhaps dawned on even military leaders, let alone political leaders of two different governments," he said.
"In retrospect, we could have perhaps prepared our soldiers better through both equipment and training."
For Canada, the war in Afghanistan cost the lives of 158 soldiers, one diplomat, one journalist and two civilian contractors.
But the losses weren't confined to the borders of Afghanistan.
Soldiers returning home faced harrowing personal battles. The recent spate of suicides of Afghan vets created a national sense of urgency about post-traumatic stress disorder and many Canadians, including federal opposition parties, are demanding better care for Canada's military personnel.
Former chief of defence staff Rick Hillier is among them.
In December, he said the suicides were a tragic and needless loss of life, saying "young men and women have lost confidence in our country to support them" and called for a public board of inquiry into the Canadian Forces' handling of mental health issues.
It's also something that weighs on MacKay's mind.
"I wish we could have, perhaps, been able to reach out into our country's mental health providers to enlist their support that's needed now," MacKay said.
Creating a 'security umbrella'
But the cabinet minister also noted the government has made ambitious efforts to do that, including doubling the complement of mental health professionals and setting up joint personnel support units.
"We have 20-year-old veterans in this country that are battle-hardened, that are combat veterans, this is something we haven't seen in a generation. And that has been a shock to the country's collective system."
More than 40,000 Canadian Forces members have been deployed to Afghanistan since October 2001.
Military operations wrapped up in 2011 and Canadian efforts were dedicated to training Afghan soldiers, along with peace-building and humanitarian development.
Creating that security umbrella, MacKay said, is the root of Canada's participation in Afghanistan.
"That's perhaps the biggest challenge … the lack of governance and the undeniable corruption," he said, adding that Canada will continue to support front-line agencies and government departments in the country.
The last group of Canadian soldiers involved in the NATO training mission were welcomed home on March 18, at a ceremony where Prime Minister Stephen Harper designated May 9 as a national day of honour to commemorate Canada's mission in Afghanistan.
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