Their reaction, in a nutshell: don't let the door hit you on the way out.
In a message sent to the entire federal bureaucracy, Harper thanked government workers for the support they've shown his team over three successive Parliaments and for their dedication to the well-being of Canadians.
In the letter, Harper expresses pride in the work he and his team have done with the public service to improve the prosperity, security and well-being of Canadians and improve Canada's position in the world.
In response, one of the biggest unions representing workers lamented the tension-filled relationship between the civil service and Harper's Conservatives.
"The work that public service workers do on behalf of Canadians day in and day out is invaluable,'' Public Service Alliance of Canada national president Robyn Benson said in a statement.
"It is unfortunate that the Conservative government was not able to recognize the important contribution of public service workers during their mandate.
"We look forward to building a positive and constructive relationship with the new Liberal government where trust and respect for public service workers is restored.''
Among the unfinished business Harper leaves behind is the renewal of contracts for hundreds of thousands of civil servants; the two sides have been locked in a protracted battle over a number of factors, including sick leave and pensions.
The failed contract talks were the latest irritant in a series of clashes during the Harper era, including the loss of 20,000 public sector jobs and complaints that civil servants were either muzzled or forced to play partisan roles.
In his letter, Harper makes no mention of the tension.
"I would like to thank each and every one of you for the support you have shown my team and me over three successive Parliaments and for the dedication you have demonstrated in delivering for Canadians,'' he wrote in the letter, obtained by The Canadian Press.
"It has been an honour to serve as prime minister of the greatest country in the world and I will always be grateful for the support of Canada's world-class public service.''
Harper officially resigns as prime minister on Wednesday, just ahead of the swearing-in of Liberal prime minister-designate Justin Trudeau.
On Thursday, Harper is expected to address the Conservative caucus, now in opposition, before they elect an interim leader; Harper stepped away from the leadership on election night.
He is still the member of Parliament for his riding of Calgary Heritage, but it's unclear whether he'll cast a ballot for his temporary political replacement.
-- With files from Terry Pedwell
Also on HuffPost