The letters by Julian Fantino, the minister responsible for the Canadian International Development Agency, or CIDA, were posted to the departmental website in December.
They appeared to violate a number of government communications policies designed to ensure that the taxpayer-funded civil service is not used for partisan purposes.
One Fantino letter was posted under a headline reading "Dear NDP: CIDA Does Not Need Your Economic Advice."
Another took the Liberals to task and contrasted their policies with those of the Conservatives.
A spokesman for Fantino told The Canadian Press in an email that the letters were "posted in error" and that CIDA "has been asked to remove them immediately."
After a link to the CIDA website appeared on Twitter late Tuesday afternoon, experts in public administration weighed in, calling the NDP letter a clear breach of the rules.
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Jonathan Rose, a political science professor at Queen's University in Kingston who helps enforce an Ontario government policy on non-partisan advertising, wrote that the letter "seems to violate every single one of the Treasury Board principles" on government communications.
And NDP Leader Tom Mulcair told CBC he had never seen anything like it posted on a government website in his more than two decades in politics.
The Conservatives have been criticized before for playing fast and loose with the sometimes blurry lines designed to keep partisanship out of the bureaucracy.
The government insisted for months it was not instructing civil servants to call the Government of Canada the "Harper Government" in government releases, but a series of emails obtained under access laws by The Canadian Press revealed it to be a widespread and orchestrated practice — against the advice of civil servants who felt it breached the communications policy.
The Conservatives continue to use the Harper Government nomenclature in departmental communications.
Editor's note: One of Fantino's letters was posted as a blog entry for The Huffington Post Canada.