The one-page ad says that Brussels is building a "super-state," denounces what it calls the "European Empire", calls for the strengthening of national parliaments and stands up against closer European integration.
"The European Parliament proved to be a dead end: it only represents its own ideological and institutional interests. The role of national parliaments needs to be strengthened," the ad says.
In response, Herman Grech, editor in chief of The Times of Malta, which did not run the ad, wrote on Thursday that Orbán's government had in effect "declared war on Hungary's free press. We will not sit idly by as he takes advantage of it elsewhere."
The conflict is the latest in a series of clashes between Orban and the bloc on issues ranging from his treatment of refugees to pressure on academics, judges and media.
Belgian newspaper De Standaard also refused the ad and published its own full-page ad instead, in rainbow colors symbolizing LGBT rights, with the text "Dear Viktor Orban, laws should never distinguish love from love."
Karel Verhoeven, editor-in-chief of the paper, called the anti-LGBT law "a blatant violation of human rights."
Two other newspapers in Belgium, La Libre Belgique and De Morgen, also refused to print the ad.
It was printed by newspapers Le Figaro in France, ABC in Spain, Jyllands-Posten in Denmark and Mlada fronta Dnes in the Czech Republic.
The Hungarian government did not respond to questions from Reuters about how many news outlets they approached and how many agreed to print the ad. "The ad is a way for us to tell in a clear and simple manner what we think is right about the future of the EU," a Hungarian government spokesman told Reuters.