Yoga has no place "in the life of Christians," the governing body of the Church has ruled.
It said it intervened after Greek media recommended yoga as a way to combat stress during coronavirus quarantine.
Other religions have also advised against the practice in the past.
The Orthodox Church is an influential organisation in Greece, and 90% of Greeks identify as Orthodox, according to a 2017 Pew Research Centre report.
"[Yoga] is a fundamental chapter in Hindu religion... it is not a 'kind of physical exercise'," the Holy Synod said in its statement on Wednesday.
Although it is not unheard of for religious authorities to criticise yoga, correspondents say it is unusual for the Orthodox Holy Synod to issue a public statement on the matter.
