Seehofer, who heads up the centre-right Christian Socialists (CSU) - Chancellor Angela Merkel's Bavarian allies - used the traditional day of drinking and political plain-talking to attack what he said was the EU's overbearing desire to control and rule the continent.
"This urge by the European Commission is strangling the European idea," Stern quoted Seehofer as saying after drinking beers in a tent in Passau. "Get rid of this centralism and bureaucracy," he said.
The CSU vice-president Peter Gauweiler went one step further, saying that Brussels just spouts "a pile of rubbish" in English jargon.
He went on to compare EU leaders in Brussels to characters in the cautionary tale of the Emperor's New Clothes. They will not tell the truth that their leader is naked for fear of losing their positions.
Gauweiler said Brussels was full of "naked, stupid emperors".
On Ash Wednesday every year, German politicians are given a chance to drink a lot of beer in tents and then take to a podium to speak their minds on any subject, or even crack a few jokes about their opponents.
This year, with the two biggest traditional adversaries the Union (CDU/CSU) and the Social Democrats (SPD) locked in the ruling grand coalition, politicians had to look elsewhere to vent their spleen.
Yet this close to the European elections in May, the comments will raise eyebrows in pro-European Germany.
They come just weeks after the Bavarian-based CSU made headlines with calls to tighten immigration policy and tackle benefit fraud by foreigners.
Seehofer and his party were keenly watching the rise of the year-old eurosceptic party Alternative für Deutschland (AfD) and he appears to be playing up attacks on Brussels to take the wind out of the AfD sails.
"Nothing is so characteristic about the CSU as their lack of character," said AfD head Bernd Lucke, speaking at his own event down the road in Osterhofen, adding that "Crazy Horst" was clearly scared of the AfD.
That is why, said Lucke, he sent Peter Gauweiler into action as a "pin-up girl to keep CSU voters."
Currently polling at six percent, the AfD is thought to have a good chance of getting seats in the European parliament - particularly after Germany's highest court voted last week to remove the three percent hurdle needed to win seats.