The investigation involves former Quebec provincial police director Richard Deschênes, as well as Jean Audette and Steven Chabot, who were responsible for criminal investigations for the Sûreté du Québec.
Chabot is retired, but Deschênes and Audette were both relieved of their duties when provincial police head Mario Laprise alerted Public Security Minister Stéphane Bergeron.
Bergeron told a news conference Wednesday that the allegations came to light when Laprise was doing a routine check of the accounting books, and discovered some unaccounted for money.
According to the minister, the money was in a fund set up to discreetly pay police informants or cover the cost of drugs in undercover operations.
He said a high-ranking officer authorized the use of money from that fund to pay someone's retirement bonus. Bergeron would not name the individual who benefited from the alleged bonus.
Officers could face criminal charges
Bergeron called the allegations "deeply troubling."
"If public funds have been misused, there will be legal action," said Jacqueline Aubé, press attaché for Bergeron.
Aubé pointed out that the three men are innocent until proven guilty, and so far, no one has been convicted.
In October, the Parti Québécois replaced Deschênes with Laprise in hopes his experience would help the government take a tougher stance on fighting organized crime in the province.
A special prosecutor and a team of retired police officers have been appointed by the public security minister to investigate the allegations. If they are found to be true, Bergeron said the officers could face criminal charges, including fraud and breach of trust.
None of the three men has been charged.