OTTAWA -- The Liberal government's bid to rebuild bridges with Statistics Canada came crashing down Friday with the resignation of the chief statistician over concerns that federal information-technology arrangements are hobbling the agency.

Wayne Smith's resignation marked the second time in the last six years that the chief statistician has quit over a point of principle.

Although former chief statistician Munir Sheikh quit in 2010 over the government's decision to make the long-form census questionnaire voluntary, a member of the National Statistics Council described the two departures as parallels, because they dealt with the independence of the agency.

Smith had raised concerns about Shared Services Canada, the government's central IT department, having an effective veto over many of the statistical agency's operations. He also raised concerns about privacy, with workers outside Statistics Canada being able to access data the agency collects on Canadians.

In a letter to the council, Smith said he can't support federal initiatives to centralize IT services that effectively undermine the independence of Statistics Canada, which the government has committed to protect.

"All of you are aware of my view that this loss of independence and control is not only an apprehension, but an effective reality today, as Statistics Canada is increasingly hobbled in the delivery of its programs through disruptive, ineffective, slow and unaffordable supply of physical informatics services by Shared Services Canada," said an email copy of the letter which Smith sent to the media.

"I have made the best effort I can to have this situation remediated, but to no effect. 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."

Smith said he does not wish to preside over what he describes as the decline of a world-leading statistical office. "So I am resigning, in order to call public attention to this situation."

Smith declined to comment further when reached by phone Friday.

The chairman of the statistics council said Smith's resignation was a surprise and a "real shame" for the agency in the wake of a successful census. Ian McKinnon said it simply came down to a question of the agency's independence.

"This was not out of any desire for empire-building or because he wanted to have the authority over something like that," McKinnon said.

"The (statistics) agencies in advanced industrial economies that do well view control of their informatics infrastructure as an essential element in being an efficient, effective and independent organization and Wayne fully shared that view and believed deeply in it."

The Liberals promised in the last election campaign to give Statistics Canada more independence from government intervention and were expected to table legislation this fall to follow through on the pledge. The new government quickly reinstated the long-form census following the October election and had been touting the return of other surveys earlier this week.

Innovation Minister Navdeep Bains, responsible for Statistics Canada, thanked Smith for his services at the agency and welcomed Smith's replacement, former assistant chief statistician Anil Arora.

"We are working closely with Statistics Canada towards the reinforcement of the independence of this eminent institution, which plays an essential role in providing Canadians with accurate and reliable statistical data," Bains said in a statement.

The minister made no specific reference to Smith's complaints.

The previous Conservative government announced the creation of Shared Services Canada in 2011, saying that centralizing IT services would save taxpayers millions of dollars annually by cutting down duplication across dozens of departments. But Shared Services has faced numerous complaints from departments frustrated by outages, delays in major projects and a lack of communication that were detailed in a critical report by the auditor general earlier this year.

Among the issues with Statistics Canada was a new system to disseminate results from this year's census, which was facing delays earlier this year and requests to upgrade its data centre that Shared Services Canada has not invested in.

Statistics council member Susan McDaniel said her conversations with Smith suggested that he was optimistic the concerns about IT could be resolved. She drew a parallel to Sheikh's resignation following a dispute over the long-form census.

"It's not the same issue, but it's a parallel issue of autonomy and independence of and the expertise of the chief statistician and his colleagues," she said.

The government already exempts the Supreme Court of Canada, the Federal Court and agents of Parliament like the auditor general from oversight by Shared Services Canada.

In an message sent to Statistics Canada staff, Smith said he made every effort to convince the Liberals to exempt the agency as well, but failed to sway the government.

"I believe it is the professional duty of a national statistician to resign if the independence of the national statistical office ... is compromised," Smith wrote.

Bains spokesman Philip Proulx said protecting Statistics Canada data is a top priority for the government and Shared Services Canada has already done a "great deal" of work to modernize the IT the statistics agency relies upon.

"We are modernizing the information technology of Statistics Canada to better provide Canadians with accurate and reliable statistical data," Proulx said.