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(Adds details of departing official's letter)
By Leah Schnurr
OTTAWA, Sept 16 (Reuters) - The head of Canada's statistics agency resigned in a surprising move on Friday over concerns that the agency's independence is being compromised, making him the second top statistician to quit in recent years.
In an email sent to the members of an independent advisory board, Wayne Smith said he was stepping down as head of Statistics Canada because of concerns around changes to the agency's data infrastructure.
Statistics Canada is responsible for producing major economic reports on everything from jobs to international trade.
In an arrangement under the previous Conservative government, responsibility for StatCan's informatics infrastructure was transferred to a department that oversees information technology services across the government.
Smith said in his email that Shared Services Canada now holds an effective veto over many of the agency's decisions, including the collection, analysis and dissemination of data.
"This loss of independence and control is not only an apprehension, but an effective reality today," Smith wrote in the email seen by Reuters, adding that StatCan is increasingly hobbled by the ineffective and slow services being provided.
"I do not wish to preside over the decline of what is still, but cannot remain in these circumstances, a world leading statistical office."
Concerns about confidentiality and efficiency had troubled Smith for some time, said Ian McKinnon, chair of the National Statistics Council advisory board.
"He felt that losing control of the data infrastructure was incompatible with the continued independence of the agency."
The agency was criticized earlier this year for technological issues that delayed the release of some economic reports on its website.
Smith came to the job after Munir Sheikh resigned in protest in 2010 after the Conservatives scrapped the long-form census.
Anil Arora, who previously helped run Canada's census, will become chief statistician as of Monday, the government said.
In a nod to the concerns, Innovation Minister Navdeep Bains said the government was working closely with the agency toward the reinforcement of its independence.
The concerns voiced by Smith come on top of some hiccups with releases in the past, said Doug Porter, chief economist at BMO Capital Markets.
"It's going to raise a lot more questions than would have been in place before," said Porter.
The agency was forced to withdraw a jobs report in 2014, citing a flaw in the way the figures had been processed. The monthly report can be volatile, often prompting economists to question its validity. (Reporting by Leah Schnurr; editing by Leslie Adler and Grant McCool)