Some 1,300 delegates rallied in the northern state of Schleswig-Holstein, which goes to the polls on May 6, in a bid to sharpen the outfit's profile in Germany's fast-shifting political landscape after weeks of bad press.
Officials for the party, which says it is standing up for more transparency in politics and internet freedom, scrambled to deny allegations of extreme-right influence and neo-Nazi leanings among some of its membership.
The delegates, predominantly young men, overwhelmingly passed a motion at the two-day gathering condemning any denial of the Holocaust after a rash of remarks by a handful of Pirates appearing to flirt with historical revisionism.
"The German Pirate Party declares that the Holocaust is an indisputable part of history. To deny it or relativise it under the pretext of freedom of expression violates the principles of our party," read the motion, which was greeted with a standing ovation.
Soon after, several participants staged a walk-out during a speech by Dietmar Moews, who recently spoke of "international Jewry" - a taboo phrase with an echo of Nazi propaganda.
Other party officials had criticised in Facebook postings the level of government subsidies to Jewish groups, claimed Hitler was justified in invading Poland and compared the swift rise of the Pirates to that of the Nazis between 1928 and 1933.
Such remarks sparked a powerful backlash in the German press and soul-searching in the party ahead of the congress.
Far-right parties are only a marginal force in German politics and have no seats in the national parliament.
Although founded in 2006 in Germany on the model of a Swedish party, the Pirates first came into their own last year by capturing seats in the Berlin state legislature.
They followed up on their stunning success last month with a strong showing in the western state of Saarland.
In both cases they poached votes from the pro-business Free Democratic Party, junior partner in Chancellor Angela Merkel's ruling coalition in Berlin, which failed to clear the five-percent hurdle for representation.
"We were young, we were small but now we have written a page of history," one of the Pirates' leading lights, 24-year-old Marina Weisband, told delegates.
The party, which has about 25,000 members, is ranked fourth in Germany, with 11-percent support nationally according to an opinion poll published Sunday.
Beyond Schleswig-Holstein, the Pirates are also gunning for seats in Germany's most populous state of North Rhine-Westphalia in a poll on May 13, ahead of the general election likely in September 2013.
Voter surveys attribute the party's success to widespread dissatisfaction and boredom with politics-as-usual in Europe's top economy.