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Deputy Minister of National Defence Jody Thomas in Ottawa on Jan. 8, 2020.BLAIR GABLE/Reuters

Prime Minister Justin Trudeau has named a veteran public servant who views China as a threat to Canada as his new national security adviser in a major reshuffle of senior bureaucrats.

Jody Thomas, currently deputy minister of National Defence, replaces Vincent Rigby who left the job as the Prime Minister’s top security adviser in June after less than two years in the role.

Her appointment was one of several unveiled Wednesday in the shakeup of the federal bureaucracy’s top level. The government also named senior health department official Jacqueline Bogden to a newly created post as deputy secretary to the cabinet for emergency preparedness and COVID-19, an acknowledgment that better planning needs to be done to deal with the pandemic and natural disasters from climate change.

Ms. Thomas, who once served as an officer in Canada’s naval reserve, has held senior positions in the public service including at Passport Canada and commissioner of the Canadian Coast Guard. She is regarded as a realist on global issues including an increasingly aggressive and belligerent China.

“She comes in fully aware of the full spectrum of international challenges that Canada faces in the security domain,” retired lieutenant-general Michael Day said. “She has been a senior deputy minister for years in the security intelligence community so there is no gap.”

In frank comments to the Ottawa Conference on Defence and Security last year, Ms. Thomas warned that Beijing is turning its attention to Canada’s Northwest Passage as melting ice opens up Arctic sea lanes to shipping and resource exploitation. “We should not underestimate at all that threat of resource exploitation in the Arctic by China in particular,” Ms. Thomas told the conference. “China has a voracious appetite and will stop at nothing to feed itself, and the Arctic is one of the last domains and regions left and we have to understand it and exploit it more quickly than they can exploit it.”

She talked about how Canada is sending a signal to China when it deploys warships to the South China Sea, a vital artery for global commerce that Beijing is trying to claim as its own by building artificial islands and military installations. “The deployment of the Navy in particular to the South China Sea is one of the messages that can be sent,” Ms. Thomas said. “[The deployments] are about the rules-based order and freedom of navigation, the freedom of the seas and the fact we will not be bullied into changing the geography of the world.”

Former Canadian Security Intelligence Service director Richard Fadden, who served as national security adviser to Mr. Trudeau and Stephen Harper, said he hopes Ms. Thomas’s appointment means the Trudeau government is waking up to the threat China poses to Western democracies.

“I thought her views on China at that conference were entirely realistic and I hope it is a signal that the government is moving in that direction,” he said. “They could have said she has these views that were further ahead of the government and we are not going to make the appointment.”

As deputy at National Defence, Mr. Fadden said Ms. Thomas has had extensive dealings with the security and intelligence establishment including NATO, the Five Eyes intelligence-sharing alliance and with senior members of the United States military.

While at National Defence, Ms. Thomas, along with then-chief of the defence staff Jonathan Vance, pushed back against Global Affairs, which objected to the Canadian Armed Forces cancelling winter survival training in Canada with the Peoples’ Liberation Army in 2019.

She told a House of Commons committee in April, 2020, that the Five Eyes, including Canada, the U.S., Britain, Australia and New Zealand, concluded that “it was possibly a risk to continue with that training.”

David Perry, vice-president of the Canadian Global Affairs Institute, described Ms. Thomas as “clear-eyed and pragmatic about the reality of great power competition and Chinese and Russian strategic activity.”

Ms. Thomas, who was known to have rubbed some senior generals the wrong way for pushing hard to change the culture of sexual misconduct in the military, is being replaced by Bill Matthews.

“During a tremendously difficult time, she has been an anchor of stability at National Defence,” Mr. Day said of Ms. Thomas.

Mr. Matthews, a former senior associate deputy minister at National Defence, was deputy minister of Public Services and Procurement, the department handling the long-delayed purchase of new modern fighter jets and frigate replacements.

Mr. Trudeau also named Dan Costello, who ran intelligence assessments at Global Affairs, as his new foreign and defence adviser. David Morrison, the current foreign policy adviser, is taking over as deputy minister at International Trade as well as the Prime Minister’s personal representative for the G7 summit of major industrialized countries.

Stephanie Carvin, a former national security analyst and an associate professor of international relations at the Norman Paterson School of International Affairs, said the China challenges confronting the new national security adviser are considerable.

“Espionage and clandestine foreign interference are now seen as the priority national security threats by Canadian Security Intelligence Service, of which China is perceived as the dominant threat in the Canadian environment,” she said.

“China is also a leading source of malicious cyber activities targeting the government, research and private industry.”

Even more complex will be managing the risks of Chinese state-owned enterprises and flagship companies championed by China, such as Huawei, Prof. Carvin said, as well as the role Chinese research and capital play in emerging technologies such as artificial intelligence, 5G and 6G mobile networks and machine learning.

Editor’s note: An earlier version of this article incorrectly stated that Jody Thomas, currently deputy minister of National Defence, replaced Vincent Rigby who left the job as the Prime Minister’s top security adviser in June after less than a year in the role. In fact, it was less than two years in the role.

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