At the company’s annual general meeting 32.7% of shareholders opposed its strategic share incentive plan (SSIP) which was set to pay Peter Fankhauser a long-term bonus of up to 225% of his base salary of £703,000, worth about £1.6m a year.

Thomas Cook has responded by reducing the maximum potential payout under the SSIP to 200% and has said it will not use it this year.

If the company did use the SSIP, it would replace the existing long-term bonus scheme, known as the performance share plan (PSP), which can in exceptional circumstances pay out 200%.

This year, under the PSP, Fankhauser has been awarded a long-term bonus of 165% of his base salary, which would pay out in three years’ time if the company’s targets are achieved.

Thomas Cook said it would consult major shareholders before the SSIP is used, and on its performance targets.

Nearly 22% of shareholders also voted against the group’s future remuneration policy and 22.5% opposed the remuneration report.

Standard Life, which holds 13% of Thomas Cook shares and is the company’s second biggest shareholder, voted against the pay plans.  In a statement the company said: ‘We disagreed with the introduction of a potential payment to executives above the remuneration policy’s normal upper limit. In addition, we opposed the introduction of new elements to the remuneration plan as we strongly believe these should be dealt with in the existing policy.’

Pay packages for top executives have come under the spotlight recently, with prime minister Theresa May citing widening pay differentials between board members and other employees as a major cause for concern when she first took up the post.

Report by Pat Sweet