According to media reports, during a recent visit to Switzerland Egemen Bagis denied that there had been an Armenian genocide, adding "Let them come and arrest me."
Under Swiss law it is a crime to deny that the killings of up to 1.5 million Armenians during World War One constituted an act of genocide.
Turkey says there was no systematic campaign against the Armenians.
A Turkish Foreign Ministry official, speaking on condition of anonymity, later said Turkey had summoned the Swiss ambassador to Ankara to tell him that the probe was "unacceptable."
Compiled from agency reports
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