In a television interview recorded on Saturday (June 26) and broadcast on Sunday (June 27) Zeman said undergoing a "sex-change operation" was like self-harm.
Zeman, who has often espoused views outside the mainstream, was responding to a question about the law Hungary passed earlier this month, which bans the dissemination of content in schools deemed to promote homosexuality and gender change.
More than half of the EU's 27 member states have opposed the law but so far the Czechs have not done so. Zeman told CNN Prima the condemnation amounted to meddling in a country's internal affairs.
Unless it rows back on the law, Hungary faces a legal challenge at the EU's highest court.