In a brief to the special commission of inquiry relating to Maher Arar, CCLA General Counsel Alan Borovoy renewed the call for independent audits in the arena of national security. The commission had been established to probe what, if any, role might have been played by the RCMP and other government agencies in the 2002 U.S. deportation of Canadian citizen Maher Arar. Having been intercepted by American authorities upon his return from a trip abroad, Arar was held, interrogated without counsel, and ultimately deported to his native Syria, where he was imprisoned for several months and allegedly tortured.

As a safeguard against such mishaps in the future, Borovoy urged the commission to recommend the creation of an independent agency, with on-going access to RCMP and other government records, facilities, and personnel, to conduct self-generated audits of practices and policies relating to national security. As an additional safeguard, the CCLA General Counsel called for an explicit power on the part of the incumbent minister to direct, in writing, the RCMP in the area of national security. Even though such a power would contravene a long-standing Canadian taboo on ministerial interference with criminal investigations, the civil liberties group argued that, without such a power, Canadians could not look to the minister for adequate protection from the possibility of police abuse.