Joachim Gauck underlined the importance of Quebec in a united Canada in a speech on Saturday in Quebec City alongside Premier Philippe Couillard.
The comments drew nearly immediate criticism from the opposition Parti Quebecois.
Gauck is at the end of a Canadian tour that included stops in Ottawa and Toronto.
For his part, Couillard says he hears comments like Gauck's often during travel abroad.
He says Canadian unity is seen as a positive in other countries.
"People are happy that Canada's political environment is stable," Couillard told reporters after Gauck's speech.
"However, they recognize the very distinct character of Quebec. People know very well that Quebec was a distinct society but generally speaking people make that kind of comment. "
Speaking to a business crowd at the provincial capital's convention centre, Gauck expressed his pleasure at being in Quebec, where the last referendum on sovereignty was held in 1995.
But he made no mention the Canada-EU free-trade deal, which has faced some opposition from Germany.
"When we prepared for this visit, we learned the important and unique role played by your province," Gauck said.
"We are also pleased your province never separated from Canada."
The comments come just over a week after the referendum in Scotland, in which voters opted to remain a part of the United Kingdom.
Couillard said he had no problem with Gauck expressing his opinion and added "it does not change the internal debate."
But PQ spokeswoman Carole Poirier said Gauck shouldn't wade into such matters on a formal visit.
"I find it shocking," Poirier said. "It's a comment that wasn't necessary in the kind of speech he made here."
Poirier said Gauck's comments were different than the PQ's decision to send a delegation to observe the referendum in Scotland.
Several PQ members openly supported Scottish independence, including potential leadership candidate Bernard Drainville.
"Drainville did not go as the president," Poirier said.
"Gauck is president of his country. It's not the same."