The statement didn't offer a reason for the removal, which comes amid an especially tense time in the Canada-China relationship.
McCallum told Chinese media in the Toronto area earlier in the week that the extradition of Meng to the United States "would not be a happy outcome".
Tensions between China and the United States and its Western allies spiked last month after Canada arrested Huawei's chief financial officer, Meng Wanzhou, on a U.S. extradition request alleging she lied to banks about trade with Iran.
McCallum's comments prompted a swift backlash from opposition officials, with Conservative Party Leader Andrew Scheer declaring he would fire McCallum if he were Prime Minister. China has detained a pair of Canadians, Michael Kovrig and Michael Spavor, in the wake of Meng's arrest, and has escalated the drug sentence against Canadian national Robert Lloyd Schellenberg to the death penalty.
"Effective immediately and in keeping with standard practice, Jim Nickel, the Deputy Head of Mission at the Embassy of Canada in Beijing, will represent Canada in China as Chargé d'affaires".
McCallum's comments sowed confusion about whether the Trudeau government secretly opposes the U.S. charges against Meng, who was arrested in Vancouver in December, and whether the government was sending two different messages in Ottawa and in Beijing.
Chief Financial Officer Meng Wanzhou, at the request of the US, which has angered China.
Brock University professor Charles Burton, a former Canadian diplomat who had served two postings in China, said McCallum's comments on Meng possibly avoiding extradition had signaled to Beijing that its hard line tactics were working. "I thank him and his family for his public service over the past many years", Trudeau said. The U.S. and a broad group of ex-envoys and academics have also called for their release.
Global Affairs Canada did not immediately respond to a request for comment. "On a matter of this importance, the Canadian government has to speak with a single, clear voice".
"Two, there's an extraterritorial aspect to her case".
McCallum's mea culpa on Thursday about his comments to Chinese-language journalists was the latest development in the saga of Canada's fallout with China over Meng's arrest.
Meng was arrested December 1 at Vancouver's airport on an extradition request from the U.S. She was freed on bail by a B.C. Supreme Court judge and is due back in court on February 6.