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.
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.