The Canadian government denied a visa application for Partey, 32, who is awaiting trial in England on multiple charges of rape and sexual assault. The former Arsenal star has pleaded not guilty to all counts.
Ghana's opening match in Group L is on Wednesday against Panama in Toronto.
A statement from FIFA on Friday confirmed that Partey will not be allowed to cross the Canadian border with his team, whose World Cup base camp is in Providence, Rhode Island.
"FIFA can confirm that player Thomas Partey will be unable to travel from Ghana's team base camp in Boston, USA, to Canada for their first match against Panama on Wednesday, 17 June, as his visa application has been refused by the Canadian government," said the statement, obtained by US sports website The Athletic.
"FIFA is not involved in the immigration processes of host countries, including the adjudication of visas. As with previous FIFA events, the host government ultimately determines who receives a visa and is admitted into the country."
Partey, who currently plays for Spain's Villarreal, has scored 16 goals in 58 games for Ghana, including three during the 2026 World Cup qualifying process.
In their group-stages matches in the US, Ghana play England on June 23 in Foxborough, Massachusetts, before taking on Croatia on June 27 in Philadelphia.
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