"You have to be careful with Bayern when you go into those one-on-ones," Eichin said this week. "I have the feeling that there are double standards here."
He urged officials to not show too much respect to the league leaders and defending champions.
"I want my players and the referees to drop their respect for Bayern. They can have it before and after the game but not during the match," said Eichin, a former footballer, who honed his management teeth at Cologne's ice hockey club.
Eichin was especially critical of Bayern coach Pep Guardiola's touchline behaviour and Franck Ribery, who he believes was fortunate to stay on the pitch in recent games for kicking out at opponents after being fouled.
"Ribery should have been sent off five times already this season," Eichin said, adding that Guardiola "does what he wants on the sidelines".
Werder are no pushovers at the moment, however, having notched more wins in 2015 than in the entire first half of the campaign and have as many points since the winter break as their more illustrious opponents.
Leading striker Franco Di Santo is in sensational form, seemingly scoring at will after taking his season tally to 12 with another goal in their win over Freiburg last week.
Viktor Skripnik, who took over late last year, has quickly turned their season around but that does not necessarily guarantee respect from Bayern representatives.
"I think it may be the consequences from a puck to his head," Bayern sports director Matthias Sammer quipped in response to Eichin's comments.
"I think German referees should remember very well what he has said because it hints at manipulation."
Bayern are 11 points clear at the top of the table on 61, having lost just once in the league this season with Werder in eighth on 33.
Second-placed VfL Wolfsburg will look to bounce back from last week's shock loss at Augsburg with a win against lowly Freiburg.
Borussia Moenchengladbach, in third place a further nine points behind, host Hanover 96 while last season's runners-up Borussia Dortmund will target all three points against Cologne in their battle for a European spot after clawing their way up the table from last place earlier in the campaign.
(Editing by John O'Brien)
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