Defence Minister Harjit Sajjan is defending his department's continued prescription of an anti-malarial drug that Health Canada now agrees can cause permanent brain damage, saying troops make their own informed decisions about whether to take it.

Mr. Sajjan told reporters on Monday that the military chooses from an "evidence-based perspective" to allow soldiers to use mefloquine, the side-effects of which some have blamed for the violence in the ill-fated Somalia mission of the early 1990s.

"We do need to protect our troops when they do go into environments against malaria, that it's a very dangerous disease to be able to get and we want to make sure that we prevent that," Mr. Sajjan said. "At the same time, we want to make sure that we give our troops the right information so they can make an informed decision, so that they can protect themselves appropriately."

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Related: Canadian veterans say anti-malaria drug prescribed in Somalia ruined lives

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Other countries, including the United States, have recognized for years that mefloquine can can cause permanent brain damage.

But it was not until early August that Health Canada quietly adopted a new advisory for doctors, pharmacists and patients that says the drug can cause adverse neuropsychiatric reactions "that have been reported to continue many years after mefloquine has been stopped."

Even after that warning was issued, Veterans Affairs and Defence officials who may not have been aware of it were reassuring former soldiers that mefloquine poses no long-term danger.

The symptoms reported by some users – anxiety, paranoia, depression, hallucinations and psychotic behaviour – are similar to those experienced by troops deployed to Somalia, where Canadian soldiers beat to death a 16-year-old Somali. About 900 military members who participated in that mission were forced to take the mefloquine as part of a poorly monitored clinical trial.

Some of those veterans want an inquiry to determine what role the drug might have played in the violence. They also want the government to contact anyone who was prescribed mefloquine to determine if they have suffered long-term consequences. And they want more research to develop better diagnosis and treatment.

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The Royal Canadian Legion strongly concurs with the recommendation for more study.

"Our sailors, soldiers and airmen and women deserve to know the side effects and to receive the proper diagnosis so that they can receive the proper care as well as assisting them to link their condition for disability benefits entitlements," David Flannigan, the Legion's dominion president, said in a letter earlier this month to Veterans Affairs Minister Kent Hehr and Mr. Sajjan. "We owe our service personnel that much."

The drug accounts for about 5 per cent of all anti-malarial medications prescribed by the military – but it is given to Canadian armed forces members five times as often as to their U.S. counterparts. Although its use has declined steeply in the past decade, it was given to 15,677 Canadian soldiers between January, 2001, and March, 2012.

The Veterans Affairs department says it does not have contact information for all 700,000 Canadian veterans – just the 200,000 for whom it is providing services – so it would be impossible for it to conduct the outreach that is being requested.

The Department of National Defence does have that sort of information and could contact soldiers and former soldiers who have taken mefloquine. But, government officials said on Monday DND does not have a pharmaceutical research mandate.

Both the Conservatives and the New Democrats want the government to hold an inquiry, find veterans and soldiers who may be affected, and conduct more research.

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"These people need help," said Cathay Wagantall, the Conservative deputy critic for veterans affairs. "We need this restorative action taken on their behalf and that is something the government can do – do the inquiry, find out how many people are out there, get them the right information so they can be diagnosed properly and treated properly."

Irene Mathyssen, the NDP critic, said she has not been satisfied with the answers provided by defence officials who have appeared before the Commons Veterans Affairs committee earlier this fall. "So, absolutely, an inquiry," Ms. Mathyssen said. "We need to support and help those people who have experienced negative events and to treat the people still suffering. Do that research. We owe it to them."