The Cologne Regional Court ruled on Wednesday that the Bundesliga club must pay back in full the sponsorship payments they received from 2009 to 2011, plus interest.
Electricity provider Teldafax filed for bankruptcy in 2011 and the company's liquidator, Biner Bahr, alleged that Leverkusen had continued to accept sponsorship when they were aware of the company's financial problems.
A statement from Leverkusen expressed discontent at the court's ruling.
"We are disappointed and surprised that our arguments and facts have not been considered," said managing director Michael Schade.
"We will now wait for the verdict and then consider whether we will appeal against this judgment."
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