Mallya, who was appointed Chairman of the Board in March 2004, will cease to be the Chairman and Director with effect from June 30, Bayer CropScience said in a statement.
Commenting on the development, the company said: "Bayer CropScience Ltd regretfully accepts the voluntary resignation of Vijay Mallya as its Director and Chairman."
The company said it will appoint a new Chairman at the next Board meeting.
Mallya, who is currently wanted in India over loan default cases related to the long-defunct Kingfisher Airlines, had in March announced retirement from the post of Chairman of Sanofi India.
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He had agreed to quit as the Chairman of United Spirits Ltd in February after its new majority owner Diageo agreed to pay him Rs 515 crore and absolve him of all liabilities over alleged financial lapses at the company founded by his family.
On reasons for his move, Mallya had said that he wanted to spend more time in England closer to his children.
Bayer is a global enterprise with core competencies in the life science fields of healthcare and agriculture. In India, Bayer CropScience is into seed and crop protection business.