Discretion in prosecutorial matters and the principle of independence have been the subject of a series of decisions by the Supreme Court of Canada in the last 25 years: Nelles v. Ontario,  2 SCR 170; R. v. T. (V.)  1 SCR 749; R. v. Cook,  1 SCR 1113; Krieger v. Law Society of Alberta, 2002 SCC 65 (CanLII) ; Miazga v. Kvello Estate, 2009 3 SCC 51(CanLII) ; R. v. Nixon, 2011 SCC 34 (CanLII) ; R. v. Anderson, 2014 SCC 41 (CanLII), and more recently Sriskandarajab v. United States of America, 2012 SCC 70 (CanLII) ; Hinse v. Canada (Attorney General), 2015 2 SCC 35 (CanLII) and Henry v. British Columbia (Attorney General), 2015 SCC 24 (CanLII) .
Section 7 of the Charter protects the constitutional right of an accused to an independent prosecutor, that is to say, the right to a prosecutor who is objectively able to act independently, at every stage of the judicial process, when making decisions concerning the nature and extent of prosecutions and who can reasonably be perceived as independent.
To ensure the independence of the Military Prosecution Services, these Services should not be under the supervision of the JAG (see section 165.17of the National Defence Act below) who is the head of the legal chain of command and is both accountable and responsible to the Minister of National Defence.
Relationship to Judge Advocate General
165.17 (1) The Director of Military Prosecutions acts under the general supervision of the Judge Advocate General.
(2) The Judge Advocate General may issue general instructions or guidelines in writing in respect of prosecutions. The Director of Military Prosecutions shall ensure that they are available to the public.
(3) The Judge Advocate General may issue instructions or guidelines in writing in respect of a particular prosecution.
Given this hierarchical relationship between the Director of Military Prosecutions (DPM) and the Judge Advocate General, any notion of independence on the part of the DPM is at best illusory. To ensure both the reality and perception of true independence, the DPM should be under the supervision of the Attorney General of Canada or the Federal Director of Penal Prosecutions.