In 2006, the Australian military deemed mefloquine "a third-line drug" alternative, and over the five years from 2011 only 25 soldiers had been prescribed the drug, and only in cases of their intolerance for other alternatives. Between 2001 and 2012, 16,000 Canadian soldiers sent to Afghanistan were given the drug as a preventative measure. In 2013, the US Army banned mefloquine from use by its special forces such as the Green Berets. In autumn 2016, the UK military followed suit with their Australian peers after a parliamentary inquiry into the matter revealed that it can cause permanent side effects and brain damage.
In early December 2016, the German defence ministry removed mefloquine from the list of medications it would provide to its soldiers.
In autumn 2016, Canadian Surgeon General Brigadier General Hugh Colin MacKay told a parliamentary committee that faulty science supported the assertion that the drug has indelible noxious side effects. An expert from Health Canada named Barbara Raymond told the same committee that the evidence she had read failed to support the conclusion of indelible side effects. Canadian soldiers who took mefloquine when deployed overseas have claimed they have been left with ongoing mental health problems.
In 2020 the UK Ministry of Defence (MoD) admitted to a breach of duty regarding the use of Mefloquine. by acknowledging numerous instances of failure to assess the risks and warn of potential side effects of the drug.