[3] In the November 2014 omnibus budget bill, the 28th Canadian Ministry of Stephen Harper decided to reorganise the management structure of PHAC.

[11] Whereas formerly the deputy civil servant charged with the operation of the PHAC was identical to the CPHO, the omnibus budget bill instituted a parallel Presidential structure to govern the organisation that then could be staffed by non-medical and non-scientific personnel.

[14] On 30 July 2020, the auditor general of Canada took notice of a Globe and Mail report in which whistleblowers had participated and launched an investigation into the scandal.

[17] The PHAC controls and funds the National Microbiology Laboratory BSL4 lab at which Xiangguo Qiu and her husband Keding Cheng performed their research into dangerous infectious diseases like Ebola and the West Nile virus.

[18] In July 2019 the Chinese nationals were fired from their non-salaried positions at the University of Winnipeg and "an unknown number of her [UW] students from China were removed from the lab on July 5" after the RCMP was called in May 2019 to investigate the curious affair of a trans-Pacific shipment of BSL4-grade viruses; at the time the PHAC was not identified by the CBC as other than an interested party[19] although her LinkedIn page does list her employer since 2003 as the PHAC.

Stewart said March 2021 that the January 2021 termination of the scientists was due to a "number of review processes" initiated by the PHAC in 2018, "relating to possible breaches of security protocols".

[22] It later came to light that a soldier from the People's Liberation Army of China named Feihu Yan had worked at the NML, co-authored six scholarly papers with Qiu while s/he was employed by the Chinese Academy of Military Medical Sciences, and furthermore had been paid by the PHAC for parts of this five-year collaboration which began before "early 2016".

[24] The CBC reported in June 2021 that they had seen government documents through the Access to Information Act that revealed Qiu to have been funded by a third-party not PHAC for her Chinese travels, of which there were "at least five trips" during 2017 and 2018.

[22] The CBC had actually asked Wang Wenbin of the Ministry of Foreign Affairs (China) in June 2021 at his weekly press conference "if Qiu and Cheng were involved in espionage on behalf of the Chinese government.

[24] A former Crown prosecutor saw parallels to the 20th century Project Sidewinder, a joint RCMP-CSIS effort which found that "the Chinese government and Asian criminal gangs had been working together in drug smuggling, nuclear espionage and other criminal activities that constituted a threat to Canadian security", an inconvenient truth that the Chretien government wanted to silence.

The CPTG was an ad-hoc advisory committee composed of experts in the fields of infectious disease, microbiology, clinical pharmacology and pharmaceutical sciences.

[citation needed] The post of President is presently held by Iain Stewart, who was appointed on 21 September 2020 to replace Tina Namiesniowski.

[17] Vice-president of the Health Security Infrastructure Branch Sally Thornton[31] was also dismissed on 15 September in the midst of controversy over the disbandment of the GPHIN system.

[citation needed] The PHAC houses several bureaucrats: Because the portfolio at the PHAC crosses so many boundaries, and especially jurisdictional ones, the civil servants have evolved what are known as Special Advisory Committees (SAC), which include Federal/Provincial/Territorial (FPT) officials such as deputy ministers of health, so as to attempt to ensure a timely response to the needs of Canadians.

[citation needed] The Public Health Network Council (PHNC) is an FPT committee that is co-chaired by the deputy CPHO, Dr Howard Njoo.

The PHNC is populated by an array of directors, deputies, chiefs, experts and coordinators, from far and wide the public health guardians of Canada.

The plan describes roles, responsibilities and authorities of FPT governments for public health and emergency management, a concept of operations outlining four scalable response levels and a governance structure that aims to facilitate an efficient, timely, evidence-informed and consistent approach across jurisdictions.The PHAC headquarters are located in two pillars—one is in Ottawa, and the other is the National Microbiology Laboratory in Winnipeg, Manitoba, the location of Canada's only Level 4 microbiology lab for human health.

[49] The CEPR is responsible for possible health risks from:[50][51] The PHAC houses the Creutzfeldt-Jakob Disease Surveillance System (CJDSS) at its Ottawa headquarters.

CAEFISS receives passive reports of Adverse Events Following Immunization (AEFI) as well as engages in active monitoring of marketed vaccines in Canada.