Horst Seehofer had described the Alternative for Germany (AfD) party as “corrosive to the state” in an interview that was posted on the website.
But Germany's highest court on Tuesday ruled that by using official resources to publish the interview, Seehofer violated the AfD's chances of getting equal treatment in political competition.
The AfD's co-chief Jörg Meuthen immediately hailed the ruling as an “important contribution to political fair play in Germany”.
In the interview in September 2018, Seehofer said the AfD's MPs are “against this country”.
Germany's constitutional court noted that while the criticisms themselves were not objectionable, the minister “may not use state resources to exert a targeted influence on the political decision-making process”.
The neutrality requirement must apply both during and outside of election campaigns, because voters are informed continuously during the political process and not just during an electoral races, it noted.
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The interview has since been removed from the ministry's website.
Since its 2013 founding and entry into German parliament four years later, the AfD has repeatedly sparked uproars over its extremist positions.
Its most radical fringe was placed under police surveillance in March, and a row is simmering within the party over whether to sever links with the ultra-radical faction.