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Justin Bourque, dressed in blue prison garb and under heavy guard, stood motionless in Moncton Provincial Court as a judge read out the charges, local media reported.
In addition to three counts of first-degree murder, Bourque was charged with the attempted murder of two other Mounties who were hurt in the attacks, police said in a statement. The rampage took place late on Wednesday.
Bourque was arrested just after midnight (0300 GMT) on Friday after a massive manhunt by police, who cordoned off a large area of Moncton, a city of about 70,000 people in the East Coast province of New Brunswick.
The shooting spree was one of the worst of its kind in Canada, where gun laws are stricter than in the United States and deadly attacks on police are rare.
Eyewitness Michelle Thibodeau told the Canadian Broadcasting Corp that after several police officers moved into her backyard, Bourque emerged from a patch of trees with his hands up and said, "I'm done."
The man was unarmed, the Royal Canadian Mounted Police (RCMP) said, although weapons were found in the vicinity.
The three Mounties killed were identified as Fabrice Georges Gevaudan, 45; David Joseph Ross, 32, and Douglas James Larche, 40.
Ross, a police dog handler, was father to a 19-month-old toddler. His wife is expecting another child.
"He died doing what he loved the most. I don't think he would have wanted to die in any other way," Ross's younger half-brother, Olivier Juneau-Rousseau, tearfully told a news conference. "He did everything for his country and he took a bullet from someone he didn't even know."
The deaths prompted an outpouring of grief across Canada. The last mass killing of Canadian police took place in Mayerthorpe in the western province of Alberta in 2005 when a gunman killed four Mounties before shooting himself.
"The only way we'll get through this is by doing it together," the RCMP commander in New Brunswick, Roger Brown, said during an earlier news conference, his voice choked with emotion. "Please keep your thoughts and your prayers with us, with our families as we grieve and heal together."
Bourque, whose next court date is July 3, was named as a suspect late on Wednesday after the shootings. Police said he had no previous criminal record.
Authorities said they were alerted on Wednesday afternoon by a member of the public who spotted an armed man in camouflage clothing walking down a residential street. When police arrived, the man moved into nearby woods and opened fire.
Local media said Bourque most recently worked at a survivalist equipment store.
A Facebook page purporting to belong to Bourque was filled with posts critical of the police and those who back gun control.