The Mounties confirmed they had taken guns from homes as officers searched homes in High River's flood zone to look for flood victims, pets and anything that might pose a threat to returning residents.
An RCMP official said any guns removed from homes were not properly stored.
In a statement released Friday, the force said officers found that some gun owners had laid out their weapons in plain view as they presumably moved valuable possessions to higher ground.
The weapons were tagged for return to their owners.
"The last thing any gun owner wants is to have their guns fall into the wrong hands. Residents of High River can be assured that firearms now in possession of the RCMP are in safe hands, and will be returned to them as soon as is practically possible," said assistant commissioner Marianne Ryan.
That angered High River residents, who have been anxious to return to their homes to assess flood damage. An evacuation order for the town of about 13,000 residents was in its ninth day Friday, although it was announced some homeowners were being allowed to return Saturday.
The seizure generated opinions on all sides, including from the highest political office in the land.
"We expect that any firearms taken will be returned to their owners as soon as possible," said Stephen Harper's press secretary Carl Vallee.
"We believe the RCMP should focus on more important tasks such as protecting lives and private property."
In a statement, Tony Bernardo, executive director of the Canadian Shooting Sports Association, called it an "act of aggression."
"This ... is further proof that the RCMP have a not-so-hidden agenda to take guns away from responsible gun owners," said Bernardo, who also sits on the federal public safety minister's firearms advisory committee.
Alberta Premier Alison Redford said she was disappointed to face questions about the gun situation. She suggested there were more important issues to deal with coming out of the flood disaster.
"Let's just make it very clear, the provincial government did not take away anyone's guns," Redford said. "The RCMP went in and secured a community that had been evacuated. And as part of that work, as I understand it, they went into houses where there were firearms that weren't properly secured and, as opposed to leaving them sitting on fireplace mantles in a town that was evacuated, they secured those guns.
"There is no suggestion that people will not be able to have their guns back again, and I really hope we can focus on more important matters at hand, such as getting 12,000 people back into High River."
Linda Duncan of Edmonton, the federal NDP's sole Alberta MP, blasted the Prime Minister's Office for telling the RCMP what to do.
"We should not be directing the RCMP what to do about enforcing the law. I just think it's a completely inappropriate thing to have gotten involved in," she said in an interview.
Duncan noted that the Mounties in this instance are answerable to the provincial attorney general.
"The RCMP are put in a very difficult position right now. They have been directed to try to maintain safety and calm down the community and protect their belongings and keep people from getting riled up. The last thing they need is politicians throwing in their two cents about what they should or shouldn't be doing."
Duncan said the priority should be on getting people back into their homes, not inflaming emotions over a non-issue.
"All it's done is cause more commotion and get people upset about something when what we need to be doing is making sure their homes are secure and, if they're not, finding accommodation."
Asked about the statement from the Prime Minister's Office, Redford wouldn't get into it.
"The prime minister was in Calgary last Friday flying over High River with me and I think he saw the devastation and the impact in the community," she said. "I'm certain there are people in the Prime Minister's Office that have an opinion about this.
"I'm not going to comment any further."
— With files from Terry Pedwell and Joan Bryden in Ottawa.
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