Canada's chief statistician was warned three months before his surprising resignation last week that a showdown with the federal government was inevitable as the agency pushed for more independence, documents show.

Wayne Smith quit on Friday afternoon, and his resignation letters accused the federal government of hobbling his agency's independence by forcing Statistics Canada to use the government's central information technology system.

Behind the scenes, the National Statistics Council — an independent body of experts that advises the chief statistician —warned of future problems unless the government agreed with Statistics Canada's request that it no longer use the IT system overseen by Shared Services Canada.

In a June report obtained by The Canadian Press through the Access to Information Act, the council wrote that the Liberals' push for the agency to find new ways to collect, analyse and distribute data was at odds with the government's insistence that the agency use the new central information platform.

The June report said Statistics Canada needed to be more agile because it was facing huge challenges in a world of big data: demands for up-to-the-minute information that businesses and planners rely on, declining response rates on traditional surveys, and meeting the government's need for statistics in new policy fields.

The council argued Statistics Canada couldn't be nimble if it relied on Shared Services Canada for IT services.

"Technology deficiencies and the bureaucratic red tape with SSC are increasing risks and delays in the production of major statistical programs," the council wrote.

"If unresolved, these could inhibit the potential for innovation on the part of the agency."

The report said that Statistics Canada needed control over its IT system to prevent privacy breaches, avoid delays in getting "cutting-edge" equipment and software and ensure the on-time release of market-moving information. It also wanted to ensure online forms didn't fail — which happened to the census submissions website on the first day of online filing.

"Governments cannot tell (Statistics Canada) to be bold and innovative and then limit its technological capacity to deliver existing or develop new programming," the council wrote in the report.

The Liberals said Friday that a "great deal" of work has been done to modernize the technology the statistics agency relies upon. Innovation Minister Navdeep Bains, who is responsible for Statistics Canada, also said the government was committed to giving the agency the independence the Grits promised during last year's election campaign.

Interim Conservative leader Rona Ambrose told The Canadian Press that the current government should be able to find a solution to the situation. Ambrose was public works minister at the time the previous government announced the creation of Shared Services Canada to centralize IT services across the government.

"These kinds of things are fixable," Ambrose said.

"It's up to the government to look into it and address it, if it's possible to address it."

NDP public services critic Erin Weir called Smith's resignation a troubling development.

"The Liberals promised, in black and white, to restore Statistics Canada's independence. It's clear from Mr. Smith's comments that the current Liberal government is responsible for compromising that independence," Weir said in a statement.

Smith told his staff in a letter Friday announcing his departure that Shared Services Canada — "and anyone who can influence Shared Services Canada" — had substantial control over Statistics Canada's work.

In his resignation letter to the statistics council, Smith said he can't support federal initiatives to centralize IT services that effectively undermine the independence of Statistics Canada. He added he does not wish to preside over what he describes as the decline of a world-leading statistical office.

Keep reading