Foreign Minister Sam Okudzeto Ablakwa, in a statement, said Ghana had problems with "the highanded and extremely unfair decision" to reject a visa application by Partey, "a key member of Ghana's senior national team".
"Ghana has dispatched an official note of protest" to Canada, he said, adding tha the "note also requested that Canada reviews its unfortunate decision".
The Villarreal midfielder, who previously played for Arsenal, has pleaded not guilty to seven charges of rape and one count of sexual assault relating to allegations by four different women between 2020 and 2022.
A trial has been set for next year, allowing the 32-year-old to represent Ghana at the World Cup, but he will not be involved in Wednesday's match in Toronto.
"While respecting Canada's sovereign right to enforce its immigration laws, Ghana considers that reliance on unproven charges in the absence of a judicial determination raises fundamental questions of fairness and proportionality," said the statement.
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FIFA has confirmed that Partey would not be able to travel from Ghana's team base camp in Boston, to Canada for their opening match against Panama on on June 17th.
The 32-year-old will be eligible to play in Ghana's subsequent Group L games against England and Croatia, both taking place in the United States.