Union officials say chopping $143 million from the Canada Border Services Agency budget over the next three years will hamper its ability to catch child pornography, drugs and terrorists at the border.
The cuts represent over 1,300 jobs, including intelligence officers and front-line agents, the union said.
Cracking down on sexual offences and illegal drugs has been a key focus for the Conservatives, as has border security.
When they were elected in 2006, they increased the number of officers by 400 and since then they've added a further 1,600 new positions, according to figures provided by Public Safety.
Union president Jean Pierre Fortin said he remembers applauding those moves, but can't understand why the increases are being reversed.
"If they are changing their mind right now and are taking everything away that was positive for public security — that's why we're in front and that's why we are screaming more than the others," he said.
"We don't understand what's going on here."
The cuts will be across the country, with the Pacific, Prairie and Quebec offices each losing over 100 people.
Fortin says the public will notice the difference in waiting times at the borders, but what they won't see is the cuts behind the scenes to people who work at keeping threats out.
"I don't know if you're going to be able to see that, but certainly it's going to be less safe," he said.
A spokeswoman for Public Safety Minister Vic Toews says the government is trying to make the border more efficient.
"We will keep it open to legitimate travel and trade, but it will remain closed to criminals and terrorists," Julie Carmichael said in an e-mail.
"We will find savings by reducing unnecessary spending and duplication of work such as cruise ships that currently need to be cleared numerous times instead of just one. This is a needless waste of time and costs our tourism operators money."
The Conservatives have been examining increased use of technology at the border, which would also help save money.
In Washington earlier this month, Prime Minister Stephen Harper said information-sharing and "infobiometrics" are part of the answer to increased border security.
"We've seen this all over the place," he said. "I'm of the strong view that checking millions and millions of people, making them go through line-ups, making them go through screening, is not, in and of itself, an effective way to identify the potentially dangerous.
"We have to have more sophisticated ways of doing that."
Fortin said the union isn't against technology but the cuts will harm that too.
"If you don't have anybody feeding the data into the system, that's where we're going to have a problem," he said.
The Opposition New Democrats say technology isn't the answer.
"With fewer officers on the front lines, we will be leaving it up to computers to ask importers if they're smuggling," said trade critic Brian Masse.
"When a border services officer reviews the paperwork, they go over routing, cargo, quantities and any other criteria that would raise suspicion. Increasingly, we will leave this up to computers. It's unacceptable."
The budget clawback also raises questions about the Canada-U.S. perimeter security deal signed last year, Fortin said.
The agreement was developed to streamline the flow of goods and services across the border, while keeping the continent safe.
"On one hand, they are negotiating with the Americans to increase the level of security and they are cutting these jobs? Where does that make any sense?
"If the plan is to leave the security to the Americans, they should tell us."
The cuts to border services are part of an overall government drive to slash $5.2 billion in program spending over the next three years, and with it, about 19,200 jobs.
Around 6,000 employees have so far been notified that they're affected by the cuts, though that doesn't mean 6,000 jobs are already gone.
The system requires all employees who do a particular job to be notified, no matter how many of their positions are being eliminated.
The government has said it hopes to manage about 7,000 losses through attrition and some employees will also be given the option of moving into vacant jobs elsewhere in the public service.
About one in three of the 12,000 who will be let go are considered front line staff, but the rest are in operations, Federal Finance Minister Jim Flaherty said Thursday in Edmonton.
He says while department officials make the decisions, Canadians can be assured there won't be problems in food inspection or border protection.
"The officials and the ministers responsible are satisfied that all of the necessary functions will continue and be adequately staffed," he said.
"Many large organizations have gone a lot further than we have and the adjustment that we are making will get us back toward the number of public servants that we had before the extra hiring that happened as a result of the economic action plan — the great recession."
Before the budget, Flaherty had said the losses would be mostly to back-office operations, but the unions have disputed that.
At Veterans Affairs, at least 75 client-service agents are among 250 employees whose jobs are on the line, the president of their union said this week.
But a spokesman for the department said Thursday it is hoped the cuts can come through attrition and that services will not be affected.
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