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Quebec’s independent police watchdog has launched an investigation into allegations of criminal misconduct against the head of the Sûreté du Québec – the top provincial cop previously called in to clean up Montreal police.

Provincial Public Security Minister Geneviève Guilbault made the announcement Wednesday, saying the government suspended SQ director Martin Prud’homme with pay until the bureau of independent investigations completes its probe.

“There is obviously a presumption of innocence and we must avoid reaching hasty conclusions,” Ms. Guilbault said. “He has been temporarily removed and he hasn't been charged with anything yet.”

Ms. Guilbault declined to say if the allegations involve Mr. Prud’homme’s professional or personal life, saying only that it pertained to “criminal infractions.” She said investigators have met with Mr. Prud’homme but did not arrest him. He could not be reached for comment.

Ms. Guilbault named Mario Bouchard, one of Mr. Prud’homme’s deputies, interim SQ director.

Just last fall, Mr. Prud’homme returned to his job in charge of the SQ after wrapping up a year as interim chief of the Montreal police force where he was applauded for starting the process to clean up department. Internal disunity had riven the Montreal police, including allegations that some officers used the internal-affairs division to settle scores among rival factions, and revelations that some were conducting surveillance on reporters.

As temporary chief, Mr. Prud’homme launched a restructuring, replaced a number of senior managers, and wrote a report on the road ahead for the troubled department, even recommending his top two choices for his replacement. One of them, former SQ deputy director Sylvain Caron, was named.

City and provincial politicians from all political stripes praised his work.

However, the Montreal police was not the only force riddled with problems.

Quebec’s anti-corruption squad, UPAC – headed by Mr. Prud’homme’s father-in-law Robert Lafrenière until his retirement late last fall – was so troubled by internal leaks that the unit spent nearly two years investigating the matter. That probe led to suspicion that Guy Ouellette, a former SQ sergeant and then-Liberal member of the National Assembly, was involved in the leaks.

Mr. Ouellette was briefly arrested and detained without charges being laid in October, 2017, in connection to the leak investigation. In February, 2018, unsealed search warrants showed UPAC had met twice with Mr. Prud’homme to question him about his ties to Mr. Ouellette. Some police forces in Quebec are so intertwined, RCMP investigators had to conduct the interviews while ensuring independence, the documents showed.

Police seized Mr. Ouellette’s cellphone and computer during the arrest. He went to court and was backed by the Speaker of the National Assembly as they argued that the items were protected by parliamentary privilege. Last fall, prosecutors dropped the matter and returned the items, saying they had “new information.”

Mr. Ouellette, meanwhile, was re-elected last October, but expelled from the Liberal caucus for an unrelated allegation that he tipped off a reporter about a Liberal partisan nomination. Mr. Ouellette has denied all the leak allegations. In November, he launched a $550,000 lawsuit against the province over the 2017 UPAC arrest.

Former premier Jean Charest created UPAC eight years ago to probe a series of scandals involving the construction and engineering industry and political financing. In the spring of 2017, a leak from within UPAC revealed a continuing investigation of the fundraising activities of Liberals, including Mr. Charest.

UPAC then launched the separate investigation involving Mr. Ouellette and Mr. Prud’homme.

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