Munir Sheikh, the head of Statistics Canada, resigned Wednesday over the federal government's decision to scrap the mandatory long-form census.

Munir Sheikh, the head of Statistics Canada, announced his resignation Wednesday. (Statistics Canada)

"I want to take this opportunity to comment on a technical statistical issue which has become the subject of media discussion. This relates to the question of whether a voluntary survey can become a substitute for a mandatory census," Sheikh said in a release.

"It cannot," he said. "Under the circumstances, I have tendered my resignation to the prime minister."

The Conservative government announced at the end of June that the long-form part of the 2011 census will no longer be mandatory because of privacy concerns. Now, Canadians who receive the long form can refuse to fill it out.

Industry Minister Tony Clement acknowledged the resignation "with regret."

He maintained his defence of the government's decision to shift to voluntary disclosure in the census.

"The government took this decision because we do not believe Canadians should be forced, under threat of fines, jail, or both, to divulge extensive private and personal information," Clement said.

Sheikh said he would not comment on the advice that he and Statistics Canada gave to the government on the subject of the long-form census.

Assistant chief statistician Wayne Smith has been named the interim head of Statistics Canada.