The protest started Thursday as about 400 union members walked off the job from the Pearson Building, headquarters for the Department of Foreign Affairs.
They were followed by the walkout of another 100 foreign service officers at a dozen key Canadian missions abroad.
These include London, Paris and Dublin — destinations for a major European trip by Harper next week that includes a stop at the G8 summit.
Timothy Edwards, president of the Professional Association of Foreign Service Officers, said the new, drastic measures will continue until Treasury Board returns to the bargaining table with a meaningful offer.
After a four-month hiatus, the two sides restarted talks this week, but they broke down when Treasury Board did not come up with a new wage offer, Edwards told The Canadian Press.
"We were told they had not obtained approval, approval had not been granted by the government," Edwards said. "We were told by the top levels of government that this was a political decision."
"It's the same offer we've been looking at for a year and a half so we rejected it on the spot. There was nothing new there."
The union then decided "to escalate our pressure tactics, now specifically targeting the political level."
A spokesman for Treasury Board Secretary Tony Clement defended the government's position.
"Our government has put forward a fair offer — fair to employees and fair for taxpayers," spokesman Matthew Conway said in an emailed statement.
"The Foreign Service is a highly sought-after and well-paid posting. We expect that any job action will respect the bounds of the law."
The 1,350-member union has been without a contract since mid-2011 and has been in a legal strike position since April.
The union is trying to force Treasury Board to address a core grievance: that its members are paid $10,000 to $14,000 a year less than their counterparts who do similar work in other federal departments.
While essential workers will remain on the job, the walkouts will stall processing of immigration applications as well as things such as trade talks and ministerial visits.
"So we will now be targeting all of the government's top international priorities, as well as all cabinet-level travel, including that of the prime minister, which we hadn't touched until now," said Edwards.
Harper's office shrugged off any suggestion that his coming travel might be affected.
"The prime minister is always fully prepared for his meetings and looks forward to a productive trip," said spokesman Carl Vallee.
Edwards said there would be ramifications for the processing of immigration claims.
"It's going to mean a massive backlog and huge reduction in the pace and volume of the processing of visas and permanent resident applications in these locations."
In other missions, the job action means no work on Canadian trade priorities, market access issues, promotion of Canadian goods and services, as well as attraction of Canadian investment, he said.
Emma Welford, a Foreign Affairs spokeswoman, said the department had plans in place to deal with the work stoppages.
"The department is monitoring the situation very closely and will take any necessary action to ensure that we continue to provide services to Canadians at home and abroad," she said in an emailed statement.
"The government will do its utmost to continue to ensure service delivery in a timely fashion with the least amount of disruption to Canadians."
The union began protesting in April after declaring it was in a legal strike position. Since then, it has staged rotating activities, including a picket by well-dressed diplomats in Washington last month.
The missions involved in Thursday's walkout include Tokyo, Tel Aviv, Ramallah and Hong Kong, as well as the immigration sections at Canada's two largest visa-processing centres in Beijing and New Delhi.
The action was meant to catch the government off guard.
The labour unrest comes as Canada tries to conclude a trade deal with Europe and seeks to expand markets in Asia and the Middle East.
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