Statistics Canada's chief statistician, Wayne Smith, has resigned, citing concerns over the independence of the agency, which he says has been "hobbled" by a move to shift its information technology capabilities to an outside department.

Mr. Smith said in a memo Friday to members of the National Statistical Council that he quit due to frustration over a shift of Statscan's informatics infrastructure to Shared Services Canada. That move, he told The Globe and Mail in July, has had a "significant impact" on the agency's operations.

The troubles have had broad implications. Internal memos released this summer under an access-to-information request show a litany of concerns from Statscan staff over the impact of the transfer of IT to Shared Services. These include technical glitches that have delayed the releases of major economic reports, including the labour force survey, security risks, a lack of accountability, and a "very real risk" that more key releases scheduled this year will have to be postponed.

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Related: How big of a census nerd are you? Try our Census 2016 quiz

In Friday's memo, Mr. Smith said shifting IT to Shared Services has hurt the agency in the delivery of its programs "through disruptive, ineffective, slow and unaffordable" services.

"I cannot lend my support to government initiatives that will purport to protect the independence of Statistics Canada when, in fact, that independence has never been more compromised," he said.

In a separate memo to Statscan staff, he also cited confidentiality concerns. "At issue is my duty to protect the confidentiality of information entrusted to Statistics Canada by Canadians," he said. "It is my view that the Shared Services Canada model does not respect the provisions of the Statistics Act which does not permit that such information be in the hands of anyone who is not meaningfully an employee of Statistics Canada …. I have raised this issue and have been unsuccessful in having it addressed."

Shared Services was created by the previous government five years ago in an initiative meant to save money by centralizing IT services. The move means Canada is the only developed country whose statistical agency doesn't have control over its IT, Mr. Smith told The Globe in July.

This is the second chief statistician to quit over the matter of independence. Mr. Smith was named chief statistician in 2010 after his predecessor Munir Sheikh resigned following controversy over the federal government's decision to cancel the mandatory long-form census in favour of a voluntary household survey.

The Prime Minister's Office named Anil Arora as the new chief statistician of Statscan. Mr. Arora, currently assistant deputy minister at Health Canada's health products and food branch, will become chief statistician, effective Monday.

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Mr. Arora has been with Health Canada since 2014; he previously worked at Statscan's census division, and was the agency's assistant chief statistician from 2008 to 2010.

Navdeep Bains, federal Minister of Innovation, Science and Economic Development, whose portfolio includes Statscan, said his department is "working closely" with Statistics Canada on reinforcing the independence of the institution.

His office did not respond to questions on what it plans to do next. Mr. Bains noted that the independence of the agency is an important aspect of his mandate. "The integrity and security of Canadians' data is paramount and … modern information technology must ensure accurate and reliable statistical data.

New Democrat MP Erin Weir, his party's public services critic, said it is clear that Mr. Smith did not resign on a whim. "I think it's very concerning and it throws into question the federal government's commitment to independence and transparency," Mr. Weir said.

Mr. Weir said there are comparisons to be drawn between the problems at Shared Services and the Phoenix Payroll System, which was rolled out in February as a single, automated system for paying federal employees but has been fraught with problems.

"Both of these initiatives were efforts to achieve some savings by centralizing functions between different departments and agencies," he said. "In theory, it might be possible to save some money by centralizing IT or payrolls but the government has to implement it properly and, in both cases, implementation was botched and they have become boondoggles."

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With files from reporter Gloria Galloway in Ottawa