Michel, the youngest prime minister in Belgium's history, said during a parliamentary session on Wednesday that the 1915 mass killings "must be viewed as a genocide."
The Turkish foreign ministry said in a statement that the remarks were "neither acceptable nor excusable", adding that the Belgian leader had "politicised" the issue.
The remarks "distort the historical facts and overlook the law," the ministry said, warning of consequences for Ankara's relations with Brussels.
Michel's remarks came after the European Parliament in April adopted a resolution to recognise the Armenian genocide, which enraged Turkey.
Ankara has been on a diplomatic offensive in recent months aimed at preventing parliaments from recognising the killing as genocide for the 100th anniversary of the tragedy.
In April, Pope Francis drew Turkey's wrath after describing the killings as "the first genocide of the 20th century."
Ankara subsequently pulled its ambassador from the Vatican, as it has from Austria, Brazil and Luxembourg.
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