Edinburgh-born group chief executive Euan Sutherland indicated Mr Flowers, who departed from Co-op Bank in June 2013 following the discovery of a major financial black hole, was contracted to receive £90,000 on leaving his post.
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However, Mr Flowers, an ordained Methodist minister who was the subject of drug taking allegations last year, was contracted to meet certain conditions, such as not bringing the bank into disrepute.
Mr Sutherland said: "As soon as the [drugs] story appeared, we stopped the payments and we are going after him for the first £30,000 we had already paid."
Separately, Co-op has received more than 80,000 responses from members of the public following the launch of a campaign to get customers to have a say in its future direction.
Co-op said the findings of the research would be published at its annual general meeting in May.